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This ensured a high confidence assignment for more than 134 million fragments, leaving 46 millions of ambiguous and long fragments (>500bp) unassigned.\relax }{figure.caption.28}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {4.5}{\ignorespaces \textbf {Signal around CTCF motifs : } the human genome was scanned with a CTCF PWM and different aggregated signal densities were measured for open chromatin (red lines), mono nucleosome (blue lines), di-nucleosomes (green lines) and for a pool of mono-nucleosome fragments with di-nucleosomes fragments cut in two at their center position (violet line). \textbf {Top row :} each position of the fragments, from the start of the first read to the end of the second, were used. \textbf {Middle row :} each position of the reads were used. \textbf {Bottom row :} only one position at the read edges for open chromatin fragment and the central position of nucleosome fragment were used. The open chromatin read edges were modified by +4bp and -5bp for +strand and -strand reads respectively. The aggregated densities were measured using bin sizes of 1 (left column), 2 (middle column) and 10bp (right column).\relax }}{54}{figure.caption.29}} +\newlabel{atac_seq_ctcf_all_data}{{4.5}{54}{\textbf {Signal around CTCF motifs : } the human genome was scanned with a CTCF PWM and different aggregated signal densities were measured for open chromatin (red lines), mono nucleosome (blue lines), di-nucleosomes (green lines) and for a pool of mono-nucleosome fragments with di-nucleosomes fragments cut in two at their center position (violet line). \textbf {Top row :} each position of the fragments, from the start of the first read to the end of the second, were used. \textbf {Middle row :} each position of the reads were used. \textbf {Bottom row :} only one position at the read edges for open chromatin fragment and the central position of nucleosome fragment were used. The open chromatin read edges were modified by +4bp and -5bp for +strand and -strand reads respectively.\\ The aggregated densities were measured using bin sizes of 1 (left column), 2 (middle column) and 10bp (right column).\relax }{figure.caption.29}{}} \citation{buenrostro_transposition_2013} -\@writefile{lof}{\contentsline {figure}{\numberline {4.6}{\ignorespaces \textbf {Signal around CTCF, SP1, myc and EBF1 motifs :} the human genome was scanned with using one PWM per TF. For each TF, the open chromatin architecture was measured by considering the corrected read edges (red) and the nucleosome occupancy (blue) by considering the center of the nucleosome fagments from the nucleosome fragment dataset. The motif location is indicated by the dashed lines.\relax }}{49}{figure.caption.29}} -\newlabel{atac_seq_ctcf_sp1_myc_ebf1_footprint}{{4.6}{49}{\textbf {Signal around CTCF, SP1, myc and EBF1 motifs :} the human genome was scanned with using one PWM per TF. For each TF, the open chromatin architecture was measured by considering the corrected read edges (red) and the nucleosome occupancy (blue) by considering the center of the nucleosome fagments from the nucleosome fragment dataset. The motif location is indicated by the dashed lines.\relax }{figure.caption.29}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {4.6}{\ignorespaces \textbf {Signal around CTCF, SP1, myc and EBF1 motifs :} the human genome was scanned with using one PWM per TF. For each TF, the open chromatin architecture was measured by considering the corrected read edges (red) and the nucleosome occupancy (blue) by considering the center of the nucleosome fagments from the nucleosome fragment dataset. The motif location is indicated by the dashed lines.\relax }}{55}{figure.caption.30}} +\newlabel{atac_seq_ctcf_sp1_myc_ebf1_footprint}{{4.6}{55}{\textbf {Signal around CTCF, SP1, myc and EBF1 motifs :} the human genome was scanned with using one PWM per TF. For each TF, the open chromatin architecture was measured by considering the corrected read edges (red) and the nucleosome occupancy (blue) by considering the center of the nucleosome fagments from the nucleosome fragment dataset. The motif location is indicated by the dashed lines.\relax }{figure.caption.30}{}} \citation{adey_rapid_2010} \citation{buenrostro_transposition_2013,li_identification_2019} \citation{neph_expansive_2012} \citation{fu_insulator_2008} \citation{neph_expansive_2012} -\@writefile{toc}{\contentsline {subsection}{\numberline {4.8.2}Measuring open chromatin and nucleosome occupancy}{50}{subsection.4.8.2}} +\@writefile{toc}{\contentsline {subsection}{\numberline {4.8.2}Measuring open chromatin and nucleosome occupancy}{56}{subsection.4.8.2}} \citation{kundaje_ubiquitous_2012} \citation{nair_probabilistic_2014} -\@writefile{toc}{\contentsline {subsection}{\numberline {4.8.3}Evaluation of EMRead and EMSequence}{51}{subsection.4.8.3}} -\@writefile{lof}{\contentsline {figure}{\numberline {4.7}{\ignorespaces \textbf {Open chromatin classes around CTCF motifs :} EMRead was run without shifing but with flipping to identify different classes of footprints around 26'650 CTCF motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }}{52}{figure.caption.30}} -\newlabel{atac_seq_emread_ctcf_noshift_flip}{{4.7}{52}{\textbf {Open chromatin classes around CTCF motifs :} EMRead was run without shifing but with flipping to identify different classes of footprints around 26'650 CTCF motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. 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The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }{figure.caption.31}{}} -\@writefile{toc}{\contentsline {subsubsection}{EMRead}{53}{subsection.4.8.3}} -\@writefile{lof}{\contentsline {figure}{\numberline {4.9}{\ignorespaces \textbf {Classification performances on simulated data :} \textbf {Left} 50 different data partitions were run using EMSequence. The discovered models were then used to assign a class label to each sequence. These assigned labels were then compared to the true labels using the AUC under the ROC curve. The red line indicates the AUC value achieved by the true motifs. \textbf {Right} the 50 ROC curves corresponding to each partition. The red lines indicates the true motifs ROC curve. The curves under the diagonal are the cases where the 1st discovered class corresponded to the 2nd true class and vice-versa. For these cases, the AUC is actually the area over the curve.\relax }}{54}{figure.caption.32}} -\newlabel{atac_seq_emseq_auc_roc}{{4.9}{54}{\textbf {Classification performances on simulated data :} \textbf {Left} 50 different data partitions were run using EMSequence. The discovered models were then used to assign a class label to each sequence. These assigned labels were then compared to the true labels using the AUC under the ROC curve. The red line indicates the AUC value achieved by the true motifs. \textbf {Right} the 50 ROC curves corresponding to each partition. The red lines indicates the true motifs ROC curve. The curves under the diagonal are the cases where the 1st discovered class corresponded to the 2nd true class and vice-versa. For these cases, the AUC is actually the area over the curve.\relax }{figure.caption.32}{}} -\@writefile{toc}{\contentsline {subsubsection}{EMSequence}{54}{figure.caption.31}} -\@writefile{lof}{\contentsline {figure}{\numberline {4.10}{\ignorespaces \textbf {SP1 motifs :} partition of 15'883 801bp sequences centered on a SP1 binding site using EMSequence. The different classes are ordered by decreasing overall probability. Arrows atop of the motifs indicates tandem arrangements of SP1 motifs.\relax }}{55}{figure.caption.33}} -\newlabel{atac_seq_emseq_sp1_10class}{{4.10}{55}{\textbf {SP1 motifs :} partition of 15'883 801bp sequences centered on a SP1 binding site using EMSequence. The different classes are ordered by decreasing overall probability. Arrows atop of the motifs indicates tandem arrangements of SP1 motifs.\relax }{figure.caption.33}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {4.8.3}Evaluation of EMRead and EMSequence}{57}{subsection.4.8.3}} +\@writefile{lof}{\contentsline {figure}{\numberline {4.7}{\ignorespaces \textbf {Open chromatin classes around CTCF motifs :} EMRead was run without shifing but with flipping to identify different classes of footprints around 26'650 CTCF motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }}{58}{figure.caption.31}} +\newlabel{atac_seq_emread_ctcf_noshift_flip}{{4.7}{58}{\textbf {Open chromatin classes around CTCF motifs :} EMRead was run without shifing but with flipping to identify different classes of footprints around 26'650 CTCF motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }{figure.caption.31}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {4.8}{\ignorespaces \textbf {Open chromatin classes around CTCF motifs :} EMRead was run with shifing but with flipping to identify different classes of footprints around 26'650 CTCF motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }}{58}{figure.caption.32}} +\newlabel{atac_seq_emread_ctcf_shift_flip}{{4.8}{58}{\textbf {Open chromatin classes around CTCF motifs :} EMRead was run with shifing but with flipping to identify different classes of footprints around 26'650 CTCF motifs. The aggregation signal around the 6 different classes found are shown by decreasing class probability. The open chromatin patterns are displayed in red, the nucleosomes are displayed in blue. The aggregated DNA sequence is displayed as a logo. The y-axis ranges from the minimum to the maximum signal observed. For the DNA logo, this corresponds to 0 and 2 bits respectively.\relax }{figure.caption.32}{}} +\@writefile{toc}{\contentsline {subsubsection}{EMRead}{59}{subsection.4.8.3}} +\@writefile{lof}{\contentsline {figure}{\numberline {4.9}{\ignorespaces \textbf {Classification performances on simulated data :} \textbf {Left} 50 different data partitions were run using EMSequence. The discovered models were then used to assign a class label to each sequence. These assigned labels were then compared to the true labels using the AUC under the ROC curve. The red line indicates the AUC value achieved by the true motifs. \textbf {Right} the 50 ROC curves corresponding to each partition. The red lines indicates the true motifs ROC curve. The curves under the diagonal are the cases where the 1st discovered class corresponded to the 2nd true class and vice-versa. For these cases, the AUC is actually the area over the curve.\relax }}{60}{figure.caption.33}} +\newlabel{atac_seq_emseq_auc_roc}{{4.9}{60}{\textbf {Classification performances on simulated data :} \textbf {Left} 50 different data partitions were run using EMSequence. The discovered models were then used to assign a class label to each sequence. These assigned labels were then compared to the true labels using the AUC under the ROC curve. The red line indicates the AUC value achieved by the true motifs. \textbf {Right} the 50 ROC curves corresponding to each partition. The red lines indicates the true motifs ROC curve. The curves under the diagonal are the cases where the 1st discovered class corresponded to the 2nd true class and vice-versa. For these cases, the AUC is actually the area over the curve.\relax }{figure.caption.33}{}} +\@writefile{toc}{\contentsline {subsubsection}{EMSequence}{60}{figure.caption.32}} +\@writefile{lof}{\contentsline {figure}{\numberline {4.10}{\ignorespaces \textbf {SP1 motifs :} partition of 15'883 801bp sequences centered on a SP1 binding site using EMSequence. The different classes are ordered by decreasing overall probability. Arrows atop of the motifs indicates tandem arrangements of SP1 motifs.\relax }}{61}{figure.caption.34}} +\newlabel{atac_seq_emseq_sp1_10class}{{4.10}{61}{\textbf {SP1 motifs :} partition of 15'883 801bp sequences centered on a SP1 binding site using EMSequence. The different classes are ordered by decreasing overall probability. Arrows atop of the motifs indicates tandem arrangements of SP1 motifs.\relax }{figure.caption.34}{}} \citation{chatr-aryamontri_biogrid_2017} \citation{castro-mondragon_rsat_2017} \@setckpt{main/ch_atac-seq}{ -\setcounter{page}{57} +\setcounter{page}{63} \setcounter{equation}{6} \setcounter{enumi}{13} \setcounter{enumii}{0} \setcounter{enumiii}{0} \setcounter{enumiv}{0} \setcounter{footnote}{0} \setcounter{mpfootnote}{0} \setcounter{part}{0} \setcounter{chapter}{4} \setcounter{section}{8} \setcounter{subsection}{3} \setcounter{subsubsection}{0} \setcounter{paragraph}{0} \setcounter{subparagraph}{0} \setcounter{figure}{10} \setcounter{table}{0} \setcounter{NAT@ctr}{0} \setcounter{FBcaption@count}{0} \setcounter{ContinuedFloat}{0} \setcounter{KVtest}{0} \setcounter{subfigure}{0} \setcounter{subfigure@save}{0} \setcounter{lofdepth}{1} \setcounter{subtable}{0} \setcounter{subtable@save}{0} \setcounter{lotdepth}{1} \setcounter{lips@count}{2} \setcounter{lstnumber}{1} \setcounter{Item}{13} \setcounter{Hfootnote}{0} \setcounter{bookmark@seq@number}{0} \setcounter{AM@survey}{0} \setcounter{ttlp@side}{0} \setcounter{myparts}{0} \setcounter{parentequation}{0} \setcounter{AlgoLine}{17} \setcounter{algocfline}{1} \setcounter{algocfproc}{1} \setcounter{algocf}{1} \setcounter{float@type}{8} \setcounter{nlinenum}{0} \setcounter{lstlisting}{0} \setcounter{section@level}{0} } diff --git a/main/ch_encode_peaks.aux b/main/ch_encode_peaks.aux index c43d65f..9e96aa3 100644 --- a/main/ch_encode_peaks.aux +++ b/main/ch_encode_peaks.aux @@ -1,81 +1,97 @@ \relax \providecommand\hyper@newdestlabel[2]{} \citation{cheng_understanding_2012} \citation{cheng_understanding_2012} \citation{mathelier_jaspar_2014} \citation{kulakovskiy_hocomoco:_2016} \citation{jolma_dna-binding_2013} \citation{cheng_understanding_2012} \citation{mathelier_jaspar_2014} \citation{kulakovskiy_hocomoco:_2016} \citation{jolma_dna-binding_2013} \citation{cheng_understanding_2012} \citation{gerstein_architecture_2012} \@writefile{toc}{\contentsline {chapter}{\numberline {2}ENCODE peaks analysis}{23}{chapter.2}} \@writefile{lof}{\addvspace {10\p@ }} \@writefile{lot}{\addvspace {10\p@ }} \@writefile{loa}{\addvspace {10\p@ }} \@writefile{toc}{\contentsline {chapter}{ENCODE peaks analysis}{23}{chapter.2}} \@writefile{toc}{\contentsline {section}{\numberline {2.1}Data}{23}{section.2.1}} \@writefile{lof}{\contentsline {figure}{\numberline {2.1}{\ignorespaces \textbf {Number of peaks in GM12878} called by ENCODE for each TF ChIP-seq experiment. The different TFs are colored by type, as defined by \citep {cheng_understanding_2012} : sequence specific TF (TFSS), non specific TF (TFNS), chromatin structure (ChromStr), chromatin modifier (ChromModif), RNAPII associated factors (Pol2), RNAPIII associated factors (Pol3) and others. The horizontal dashed lines indicate 20'000 and 40'000.\relax }}{24}{figure.caption.19}} \newlabel{encode_peaks_gm12878_peak_number}{{2.1}{24}{\textbf {Number of peaks in GM12878} called by ENCODE for each TF ChIP-seq experiment. The different TFs are colored by type, as defined by \citep {cheng_understanding_2012} : sequence specific TF (TFSS), non specific TF (TFNS), chromatin structure (ChromStr), chromatin modifier (ChromModif), RNAPII associated factors (Pol2), RNAPIII associated factors (Pol3) and others. The horizontal dashed lines indicate 20'000 and 40'000.\relax }{figure.caption.19}{}} \@writefile{lof}{\contentsline {figure}{\numberline {2.2}{\ignorespaces \textbf {Proportion of peaks with a motif in GM12878}, for each TF ChIP-seq experiment, in green. Assuming that a TF binds to DNA through its motif, the motif should be nearby the peak center. Thus the center of each peak was scanned using a PWM describing the TF binding specificity. Each TF was associated to a log-odd PWM contained either in JASPAR Core vertebrate 2014 \citep {mathelier_jaspar_2014}, HOCOMOCO v10 \citep {kulakovskiy_hocomoco:_2016} or Jolma \citep {jolma_dna-binding_2013} collection. If a motif instance with a score corresponding to a pvalue higher or equal to $1\cdot 10^{-4}$ could be found, the peak was considered bearing a motif. The different TFs are colored by type, as defined by \citep {cheng_understanding_2012} : sequence specific TF (TFSS), non specific TF (TFNS), chromatin structure (ChromStr), chromatin modifier (ChromModif), RNAPII associated factors (Pol2), RNAPIII associated factors (Pol3) and others.\relax }}{24}{figure.caption.20}} \newlabel{encode_peaks_gm12878_motif_prop}{{2.2}{24}{\textbf {Proportion of peaks with a motif in GM12878}, for each TF ChIP-seq experiment, in green. Assuming that a TF binds to DNA through its motif, the motif should be nearby the peak center. Thus the center of each peak was scanned using a PWM describing the TF binding specificity. Each TF was associated to a log-odd PWM contained either in JASPAR Core vertebrate 2014 \citep {mathelier_jaspar_2014}, HOCOMOCO v10 \citep {kulakovskiy_hocomoco:_2016} or Jolma \citep {jolma_dna-binding_2013} collection. If a motif instance with a score corresponding to a pvalue higher or equal to $1\cdot 10^{-4}$ could be found, the peak was considered bearing a motif. The different TFs are colored by type, as defined by \citep {cheng_understanding_2012} : sequence specific TF (TFSS), non specific TF (TFNS), chromatin structure (ChromStr), chromatin modifier (ChromModif), RNAPII associated factors (Pol2), RNAPIII associated factors (Pol3) and others.\relax }{figure.caption.20}{}} \citation{wu_biogps:_2016} \citation{hon_chromasig:_2008} \citation{nielsen_catchprofiles:_2012} \citation{kundaje_ubiquitous_2012} \citation{nair_probabilistic_2014} \citation{groux_spar-k:_2019} \citation{nair_probabilistic_2014} \@writefile{toc}{\contentsline {section}{\numberline {2.2}ChIPPartitioning : an algorithm to identify chromatin architectures}{25}{section.2.2}} -\@writefile{toc}{\contentsline {section}{\numberline {2.3}Nucleosome organization around transcription factor binding sites}{26}{section.2.3}} -\@writefile{toc}{\contentsline {section}{\numberline {2.4}The case of CTCF, ZNF143, YY1, SMC3 and RAD21}{26}{section.2.4}} -\@writefile{toc}{\contentsline {section}{\numberline {2.5}Study of CTCF interactor motifs}{26}{section.2.5}} -\@writefile{toc}{\contentsline {section}{\numberline {2.6}The EBF1 case}{26}{section.2.6}} +\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.1}Data realignment}{27}{subsection.2.2.1}} +\@writefile{toc}{\contentsline {section}{\numberline {2.3}Nucleosome organization around transcription factor binding sites}{27}{section.2.3}} +\@writefile{lof}{\contentsline {figure}{\numberline {2.3}{\ignorespaces \textbf {Chromatin pattern around TF binding sites in GM12878 :} \textbf {A} For each peaklist, nucleosome occupancy was measured +/- 1kb around each individual TFBS using 10bp bins. The TFBS were then classified into 4 classes according to their nucleosome patterns using a ChIPPartitioning, allowing the patterns to be flipped and shifted. Each TF binding site was assigned a probability to belong to each of the 4 classes with a given values of shift and flip. To assess the extent of a given TF to i) display nucleosomes arrays on its flank and ii) to have nucleosome positioned with respect to its binding sites, array density and shift probability standard deviation have been measured for each class. Classes having a mean array density above 0.4 and a shift probability standard deviation under 3.5 and other custom classes are highlighted. Classes are named using the TF, the laboratory which produced the data and the class number (from 1 to 4). \textbf {B} Examples of class patterns corresponding to some of the highlighted classes for CTCF, ATF3, YY1, EBF1 and ZNF143. MNase profiles (red) were allowed to be shifted and flipped and DNaseI (blue), TSS density (violet) and sequence conservation (green) were overlaid according to MNase classification (taking into account both shift and flip). The y-axis scale represent the proportion of the highest signal for each chromatin pattern.\relax }}{28}{figure.caption.21}} +\newlabel{encode_peaks_array_measure}{{2.3}{28}{\textbf {Chromatin pattern around TF binding sites in GM12878 :} \textbf {A} For each peaklist, nucleosome occupancy was measured +/- 1kb around each individual TFBS using 10bp bins. The TFBS were then classified into 4 classes according to their nucleosome patterns using a ChIPPartitioning, allowing the patterns to be flipped and shifted. Each TF binding site was assigned a probability to belong to each of the 4 classes with a given values of shift and flip. To assess the extent of a given TF to i) display nucleosomes arrays on its flank and ii) to have nucleosome positioned with respect to its binding sites, array density and shift probability standard deviation have been measured for each class. Classes having a mean array density above 0.4 and a shift probability standard deviation under 3.5 and other custom classes are highlighted. Classes are named using the TF, the laboratory which produced the data and the class number (from 1 to 4). \textbf {B} Examples of class patterns corresponding to some of the highlighted classes for CTCF, ATF3, YY1, EBF1 and ZNF143. MNase profiles (red) were allowed to be shifted and flipped and DNaseI (blue), TSS density (violet) and sequence conservation (green) were overlaid according to MNase classification (taking into account both shift and flip). The y-axis scale represent the proportion of the highest signal for each chromatin pattern.\relax }{figure.caption.21}{}} +\citation{zhang_canonical_2014} +\citation{kundaje_ubiquitous_2012} +\citation{dreos_mga_2018} +\citation{gerstein_architecture_2012} +\citation{mathelier_jaspar_2014} +\citation{kulakovskiy_hocomoco:_2016} +\citation{jolma_dna-binding_2013} +\citation{gaffney_controls_2012} +\citation{boyle_high-resolution_2008} +\@writefile{toc}{\contentsline {section}{\numberline {2.4}The case of CTCF, ZNF143, YY1, SMC3 and RAD21}{30}{section.2.4}} +\@writefile{toc}{\contentsline {section}{\numberline {2.5}Study of CTCF interactor motifs}{30}{section.2.5}} +\@writefile{toc}{\contentsline {section}{\numberline {2.6}The EBF1 case}{30}{section.2.6}} +\@writefile{toc}{\contentsline {section}{\numberline {2.7}Methods}{30}{section.2.7}} +\@writefile{toc}{\contentsline {subsection}{\numberline {2.7.1}Data and data processing}{30}{subsection.2.7.1}} +\citation{dreos_eukaryotic_2017} +\citation{siepel_evolutionarily_2005} \@setckpt{main/ch_encode_peaks}{ -\setcounter{page}{27} +\setcounter{page}{32} \setcounter{equation}{0} \setcounter{enumi}{13} \setcounter{enumii}{0} \setcounter{enumiii}{0} \setcounter{enumiv}{0} \setcounter{footnote}{0} \setcounter{mpfootnote}{0} \setcounter{part}{0} \setcounter{chapter}{2} -\setcounter{section}{6} -\setcounter{subsection}{0} +\setcounter{section}{7} +\setcounter{subsection}{1} \setcounter{subsubsection}{0} \setcounter{paragraph}{0} \setcounter{subparagraph}{0} -\setcounter{figure}{2} +\setcounter{figure}{3} \setcounter{table}{0} \setcounter{NAT@ctr}{0} \setcounter{FBcaption@count}{0} \setcounter{ContinuedFloat}{0} \setcounter{KVtest}{0} \setcounter{subfigure}{0} \setcounter{subfigure@save}{0} \setcounter{lofdepth}{1} \setcounter{subtable}{0} \setcounter{subtable@save}{0} \setcounter{lotdepth}{1} \setcounter{lips@count}{2} \setcounter{lstnumber}{1} \setcounter{Item}{13} \setcounter{Hfootnote}{0} \setcounter{bookmark@seq@number}{0} \setcounter{AM@survey}{0} \setcounter{ttlp@side}{0} \setcounter{myparts}{0} \setcounter{parentequation}{0} \setcounter{AlgoLine}{0} \setcounter{algocfline}{0} \setcounter{algocfproc}{0} \setcounter{algocf}{0} \setcounter{float@type}{8} \setcounter{nlinenum}{0} \setcounter{lstlisting}{0} \setcounter{section@level}{0} } diff --git a/main/ch_encode_peaks.log b/main/ch_encode_peaks.log index c315f57..4743fa3 100644 --- a/main/ch_encode_peaks.log +++ b/main/ch_encode_peaks.log @@ -1,3936 +1,12230 @@ -This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex 2018.12.12) 24 OCT 2019 10:48 +This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex 2018.12.12) 25 OCT 2019 16:48 entering extended mode restricted \write18 enabled. %&-line parsing enabled. **ch_encode_peaks.tex (./ch_encode_peaks.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. ! 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LaTeX Error: Missing \begin{document}. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.8 I + t is now clear that nucleosome occupancy fulfils more than a packaging ... + +You're in trouble here. Try typing to proceed. +If that doesn't work, type X to quit. + +Missing character: There is no I in font nullfont! +Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! 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Missing character: There is no n in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no , in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no v in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! -Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no a in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no I in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no c in font nullfont! -Missing character: There is no o in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no b in font nullfont! Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! -Missing character: There is no - in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no D in font nullfont! +Missing character: There is no N in font nullfont! +Missing character: There is no A in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no s in font nullfont! +Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no q in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no c in font nullfont! Missing character: There is no u in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no . in font nullfont! + +Overfull \hbox (20.0pt too wide) in paragraph at lines 8--9 +[] + [] + + +! LaTeX Error: Missing \begin{document}. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.10 A + s discussed above, the organization of chromatin has a deep impact on ... + +You're in trouble here. Try typing to proceed. +If that doesn't work, type X to quit. + +Missing character: There is no A in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! -Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! -Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no z in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! -Missing character: There is no . in font nullfont! -Missing character: There is no T in font nullfont! +Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! -Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no u in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no y in font nullfont! -Missing character: There is no b in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no v in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no F in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! -Missing character: There is no u in font nullfont! -Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no N in font nullfont! +Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! -Missing character: There is no u in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no g in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no F in font nullfont! Missing character: There is no s in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no h in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no u in font nullfont! +Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no r in font nullfont! 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Missing character: There is no o in font nullfont! -Missing character: There is no k in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no k in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! 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Missing character: There is no a in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no y in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no r in font nullfont! Missing character: There is no i in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! +Missing character: There is no v in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no d in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no u in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no x in font nullfont! Missing character: There is no p in font nullfont! -Missing character: There is no - in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no a in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no c in font nullfont! +Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no m in font nullfont! -Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no s in font nullfont! +Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! -Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no f in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no t in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no c in font nullfont! 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Missing character: There is no i in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no m in font nullfont! -Missing character: There is no - in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no b in font nullfont! +Missing character: There is no c in font nullfont! 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Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! -Missing character: There is no e in font nullfont! 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Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no a in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no h in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! -Missing character: There is no t in font nullfont! +Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no u in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 13--14 +Overfull \hbox (20.0pt too wide) in paragraph at lines 10--11 [] [] +! Undefined control sequence. +l.12 \section + {Data} +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. -Overfull \hbox (7.67015pt too wide) in paragraph at lines 13--14 -\OML/cmm/m/it/10 R$ - [] - - -Overfull \hbox (21.64581pt too wide) in paragraph at lines 13--14 -\OML/cmm/m/it/10 NxL$ - [] - - -Overfull \hbox (9.12497pt too wide) in paragraph at lines 13--14 -\OML/cmm/m/it/10 N$ - [] - - -Overfull \hbox (51.75833pt too wide) in paragraph at lines 13--14 -\OML/cmm/m/it/10 r[]; r[]; :::; r[]$ - [] - - -Overfull \hbox (6.80557pt too wide) in paragraph at lines 13--14 -\OML/cmm/m/it/10 L$ - [] - - -Overfull \hbox (19.76384pt too wide) in paragraph at lines 13--14 -\OML/cmm/m/it/10 K \OMS/cmsy/m/n/10 ^^T - [] - - -Overfull \hbox (9.12497pt too wide) in paragraph at lines 13--14 -\OML/cmm/m/it/10 N$ - [] - - -Overfull \hbox (20.16664pt too wide) in paragraph at lines 13--14 -\OML/cmm/m/it/10 L[] \OMS/cmsy/m/n/10 ^^T - [] +! LaTeX Error: Missing \begin{document}. -Overfull \hbox (6.80557pt too wide) in paragraph at lines 13--14 -\OML/cmm/m/it/10 L$ - [] +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.12 \section{D + ata} +You're in trouble here. Try typing to proceed. +If that doesn't work, type X to quit. +Missing character: There is no D in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! -Overfull \hbox (9.12497pt too wide) in paragraph at lines 13--14 -\OML/cmm/m/it/10 N$ +Overfull \hbox (20.0pt too wide) in paragraph at lines 12--13 +[] [] -Overfull \hbox (7.67015pt too wide) in paragraph at lines 13--14 -\OML/cmm/m/it/10 R$ - [] - +! LaTeX Error: Environment figure undefined. -Overfull \hbox (9.20833pt too wide) in paragraph at lines 13--14 -\OML/cmm/m/it/10 K$ - [] +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.15 \begin{figure} + +Your command was ignored. +Type I to replace it with another command, +or to continue without it. ! LaTeX Error: Missing \begin{document}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.15 B - ecause of the technical limitations of the sequencing library preparat... - +l.16 \begin{center} + You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. -Missing character: There is no B in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no u in font nullfont! + +Overfull \hbox (20.0pt too wide) in paragraph at lines 16--16 +[] + [] + +! Undefined control sequence. +l.17 \includegraphics + [scale=0.3]{images/ch_encode_peaks/peaklist_peaknumber... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +Missing character: There is no [ in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no = in font nullfont! +Missing character: There is no 0 in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no 3 in font nullfont! +Missing character: There is no ] in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no / in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +! Missing $ inserted. + + $ +l.17 \includegraphics[scale=0.3]{images/ch_ + encode_peaks/peaklist_peaknumber... +I've inserted a begin-math/end-math symbol since I think +you left one out. Proceed, with fingers crossed. + +LaTeX Font Info: External font `cmex10' loaded for size +(Font) <7> on input line 17. +LaTeX Font Info: External font `cmex10' loaded for size +(Font) <5> on input line 17. +! Extra }, or forgotten $. +l.17 ...ode_peaks/peaklist_peaknumber_GM12878.png} + +I've deleted a group-closing symbol because it seems to be +spurious, as in `$x}$'. But perhaps the } is legitimate and +you forgot something else, as in `\hbox{$x}'. In such cases +the way to recover is to insert both the forgotten and the +deleted material, e.g., by typing `I$}'. + +! Undefined control sequence. +l.18 \captionof + {figure}{\textbf{Number of peaks in GM12878} called by ENCOD... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +! Undefined control sequence. +l.18 ... are colored by type, as defined by \citep + {cheng_understanding_2012}... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + + +! LaTeX Error: Command \end{center} invalid in math mode. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.20 \end{center} + +Try typing to proceed. +If that doesn't work, type X to quit. + + +! LaTeX Error: Something's wrong--perhaps a missing \item. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.20 \end{center} + +Try typing to proceed. +If that doesn't work, type X to quit. + + +! LaTeX Error: Something's wrong--perhaps a missing \item. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.20 \end{center} + +Try typing to proceed. +If that doesn't work, type X to quit. + +! Missing $ inserted. + + $ +l.20 \end{center} + +I've inserted something that you may have forgotten. +(See the above.) +With luck, this will get me unwedged. But if you +really didn't forget anything, try typing `2' now; then +my insertion and my current dilemma will both disappear. + +! Missing } inserted. + + } +l.20 \end{center} + +I've inserted something that you may have forgotten. +(See the above.) +With luck, this will get me unwedged. But if you +really didn't forget anything, try typing `2' now; then +my insertion and my current dilemma will both disappear. + + +! LaTeX Error: \begin{document} ended by \end{figure}. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.21 \end{figure} + +Your command was ignored. +Type I to replace it with another command, +or to continue without it. + + +Overfull \hbox (2104.56148pt too wide) in paragraph at lines 17--22 +[]\OML/cmm/m/it/10 ncode[]eaks=peaklist[]eaknumber[]M\OT1/cmr/m/n/10 12878\OML/ +cmm/m/it/10 :png[][][]$ + [] + + +! LaTeX Error: Environment figure undefined. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.24 \begin{figure} + +Your command was ignored. +Type I to replace it with another command, +or to continue without it. + + +Overfull \hbox (20.0pt too wide) in paragraph at lines 25--25 +[] + [] + +! Undefined control sequence. +l.26 \includegraphics + [scale=0.3]{images/ch_encode_peaks/peaklist_proportion... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +Missing character: There is no [ in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no = in font nullfont! +Missing character: There is no 0 in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no 3 in font nullfont! +Missing character: There is no ] in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no / in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +! Missing $ inserted. + + $ +l.26 \includegraphics[scale=0.3]{images/ch_ + encode_peaks/peaklist_proportion... +I've inserted a begin-math/end-math symbol since I think +you left one out. Proceed, with fingers crossed. + +! Extra }, or forgotten $. +l.26 ...de_peaks/peaklist_proportions_GM12878.png} + +I've deleted a group-closing symbol because it seems to be +spurious, as in `$x}$'. But perhaps the } is legitimate and +you forgot something else, as in `\hbox{$x}'. In such cases +the way to recover is to insert both the forgotten and the +deleted material, e.g., by typing `I$}'. + +! Undefined control sequence. +l.27 \captionof + {figure}{\textbf{Proportion of peaks with a motif in GM12878... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +! Undefined control sequence. +l.27 ...ther in JASPAR Core vertebrate 2014 \citep + {mathelier_jaspar_2014}, H... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +! Undefined control sequence. +l.27 ...athelier_jaspar_2014}, HOCOMOCO v10 \citep + {kulakovskiy_hocomoco:_201... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +! Undefined control sequence. +l.27 ...ulakovskiy_hocomoco:_2016} or Jolma \citep + {jolma_dna-binding_2013} c... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +! Missing } inserted. + + } +l.27 ...esponding to a pvalue higher or equal to $ + 1\cdot10^{-4}$ could be fo... +I've inserted something that you may have forgotten. +(See the above.) +With luck, this will get me unwedged. But if you +really didn't forget anything, try typing `2' now; then +my insertion and my current dilemma will both disappear. + +Missing character: There is no 1 in font nullfont! +! Missing $ inserted. + + $ +l.27 ...ing to a pvalue higher or equal to $1\cdot + 10^{-4}$ could be found, t... +I've inserted a begin-math/end-math symbol since I think +you left one out. Proceed, with fingers crossed. + +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no k in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no F in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no y in font nullfont! +! Undefined control sequence. +l.27 ... are colored by type, as defined by \citep + {cheng_understanding_2012}... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +! Missing $ inserted. + + $ +l.27 ...lored by type, as defined by \citep{cheng_ + understanding_2012} : sequ... +I've inserted a begin-math/end-math symbol since I think +you left one out. Proceed, with fingers crossed. + +! Extra }, or forgotten $. +l.27 ...efined by \citep{cheng_understanding_2012} + : sequence specific TF (T... +I've deleted a group-closing symbol because it seems to be +spurious, as in `$x}$'. But perhaps the } is legitimate and +you forgot something else, as in `\hbox{$x}'. In such cases +the way to recover is to insert both the forgotten and the +deleted material, e.g., by typing `I$}'. + +! Extra }, or forgotten $. +l.27 ...III associated factors (Pol3) and others.} + +I've deleted a group-closing symbol because it seems to be +spurious, as in `$x}$'. But perhaps the } is legitimate and +you forgot something else, as in `\hbox{$x}'. In such cases +the way to recover is to insert both the forgotten and the +deleted material, e.g., by typing `I$}'. + + +! LaTeX Error: Command \end{center} invalid in math mode. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.29 \end{center} + +Try typing to proceed. +If that doesn't work, type X to quit. + + +! LaTeX Error: Something's wrong--perhaps a missing \item. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.29 \end{center} + +Try typing to proceed. +If that doesn't work, type X to quit. + + +! LaTeX Error: Something's wrong--perhaps a missing \item. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.29 \end{center} + +Try typing to proceed. +If that doesn't work, type X to quit. + +! Missing $ inserted. + + $ +l.29 \end{center} + +I've inserted something that you may have forgotten. +(See the above.) +With luck, this will get me unwedged. But if you +really didn't forget anything, try typing `2' now; then +my insertion and my current dilemma will both disappear. + +! Missing } inserted. + + } +l.29 \end{center} + +I've inserted something that you may have forgotten. +(See the above.) +With luck, this will get me unwedged. But if you +really didn't forget anything, try typing `2' now; then +my insertion and my current dilemma will both disappear. + +! Missing } inserted. + + } +l.29 \end{center} + +I've inserted something that you may have forgotten. +(See the above.) +With luck, this will get me unwedged. But if you +really didn't forget anything, try typing `2' now; then +my insertion and my current dilemma will both disappear. + + +! LaTeX Error: \begin{document} ended by \end{figure}. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.30 \end{figure} + +Your command was ignored. +Type I to replace it with another command, +or to continue without it. + + +Overfull \hbox (2676.67934pt too wide) in paragraph at lines 26--31 +[]\OML/cmm/m/it/10 ncode[]eaks=peaklist[]roportions[]M\OT1/cmr/m/n/10 12878\OML +/cmm/m/it/10 :png[][]$$\OMS/cmsy/m/n/10 ^^A\OT1/cmr/m/n/10 10[]$ + [] + + +Overfull \hbox (89.93146pt too wide) in paragraph at lines 26--31 +[]\OML/cmm/m/it/10 nderstanding[]\OT1/cmr/m/n/10 012 : + [] + + +Overfull \hbox (907.9273pt too wide) in paragraph at lines 26--31 +\OML/cmm/m/it/10 sequencespecificTF\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 TFSS\OT1/c +mr/m/n/10 )\OML/cmm/m/it/10 ; nonspecificTF\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 TF +NS\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 ; chromatinstructure\OT1/cmr/m/n/10 (\OML/c +mm/m/it/10 ChromStr\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 ; chromatinmodifier\OT1/cm +r/m/n/10 (\OML/cmm/m/it/10 ChromModif\OT1/cmr/m/n/10 )\OML/cmm/m/it/10 ; RNAPII +associatedfactors\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 Pol\OT1/cmr/m/n/10 2)\OML/cm +m/m/it/10 ; RNAPIIIassociatedfactors\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 Pol\OT1/c +mr/m/n/10 3)\OML/cmm/m/it/10 andothers:[]$ + [] + +Missing character: There is no I in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no z in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no E in font nullfont! +Missing character: There is no N in font nullfont! +Missing character: There is no C in font nullfont! +Missing character: There is no O in font nullfont! +Missing character: There is no D in font nullfont! +Missing character: There is no E in font nullfont! +Missing character: There is no C in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no - in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no . in font nullfont! + +Overfull \hbox (20.0pt too wide) in paragraph at lines 32--35 +[] + [] + +Missing character: There is no T in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no G in font nullfont! +Missing character: There is no M in font nullfont! +Missing character: There is no 1 in font nullfont! +Missing character: There is no 2 in font nullfont! +Missing character: There is no 8 in font nullfont! +Missing character: There is no 7 in font nullfont! +Missing character: There is no 8 in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no G in font nullfont! +Missing character: There is no M in font nullfont! +Missing character: There is no 1 in font nullfont! +Missing character: There is no 2 in font nullfont! +Missing character: There is no 8 in font nullfont! +Missing character: There is no 7 in font nullfont! +Missing character: There is no 8 in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no - in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no B in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! 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+Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no k in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! 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+Missing character: There is no l in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no - in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no o in font nullfont! 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+Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no E in font nullfont! +Missing character: There is no N in font nullfont! +Missing character: There is no C in font nullfont! +Missing character: There is no O in font nullfont! +Missing character: There is no D in font nullfont! +Missing character: There is no E in font nullfont! +Missing character: There is no C in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no C in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no I in font nullfont! +Missing character: There is no P in font nullfont! +Missing character: There is no - in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no q in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no 5 in font nullfont! +Missing character: There is no 3 in font nullfont! 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Undefined control sequence. +l.43 \section + {ChIPPartitioning : an algorithm to identify chromatin architec... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). 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+Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! + +Overfull \hbox (20.0pt too wide) in paragraph at lines 43--44 +[] + [] + +Missing character: There is no D in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no - in font nullfont! 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+Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! 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+Missing character: There is no - in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no ' in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no F in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no r in font nullfont! 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+Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no M in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no g in font nullfont! 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+Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no - in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! 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+Missing character: There is no e in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no D in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no s in font nullfont! +! Undefined control sequence. +l.49 ...e last decade. Dedicated algorithms \citep + {hon_chromasig:_2008} \cit... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +Missing character: There is no h in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +! Missing $ inserted. + + $ +l.49 ...t decade. Dedicated algorithms \citep{hon_ + chromasig:_2008} \citep{ni... +I've inserted a begin-math/end-math symbol since I think +you left one out. Proceed, with fingers crossed. + +! Extra }, or forgotten $. +l.49 ...ted algorithms \citep{hon_chromasig:_2008} + \citep{nielsen_catchprofi... +I've deleted a group-closing symbol because it seems to be +spurious, as in `$x}$'. But perhaps the } is legitimate and +you forgot something else, as in `\hbox{$x}'. In such cases +the way to recover is to insert both the forgotten and the +deleted material, e.g., by typing `I$}'. + +! Undefined control sequence. +l.49 ...orithms \citep{hon_chromasig:_2008} \citep + {nielsen_catchprofiles:_20... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +! Undefined control sequence. +l.49 ...\citep{nielsen_catchprofiles:_2012} \citep + {kundaje_ubiquitous_2012} ... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +! Undefined control sequence. +l.49 ...12} \citep{kundaje_ubiquitous_2012} \citep + {nair_probabilistic_2014} ... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +! Undefined control sequence. +l.49 ...12} \citep{nair_probabilistic_2014} \citep + {groux_spar-k:_2019} have ... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +! Missing $ inserted. + + $ +l.50 + +I've inserted a begin-math/end-math symbol since I think +you left one out. Proceed, with fingers crossed. + + +Overfull \hbox (20.0pt too wide) in paragraph at lines 49--50 +[] + [] + + +Overfull \hbox (56.84067pt too wide) in paragraph at lines 49--50 +[]\OML/cmm/m/it/10 hromasig \OT1/cmr/m/n/10 :[] + [] + + +Overfull \hbox (892.81776pt too wide) in paragraph at lines 49--50 +\OT1/cmr/m/n/10 008[][][][]\OML/cmm/m/it/10 havebeendevelopedtoclustergenomicre +gionsbasedontheirdistributionofreads; whichreflectstheirfunction:$ + [] + +Missing character: There is no M in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no H in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no y in font nullfont! +! Undefined control sequence. +l.53 ...robabilistic algorithm developed by \citep + {nair_probabilistic_2014},... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no r in font nullfont! +! Missing $ inserted. + + $ +l.53 ...listic algorithm developed by \citep{nair_ + probabilistic_2014}, which... +I've inserted a begin-math/end-math symbol since I think +you left one out. Proceed, with fingers crossed. + +! Extra }, or forgotten $. +l.53 ...veloped by \citep{nair_probabilistic_2014} + , which we will call ChIPP... +I've deleted a group-closing symbol because it seems to be +spurious, as in `$x}$'. But perhaps the } is legitimate and +you forgot something else, as in `\hbox{$x}'. In such cases +the way to recover is to insert both the forgotten and the +deleted material, e.g., by typing `I$}'. + +! Missing $ inserted. + + $ +l.54 + +I've inserted a begin-math/end-math symbol since I think +you left one out. Proceed, with fingers crossed. + + +Overfull \hbox (20.0pt too wide) in paragraph at lines 53--54 +[] + [] + + +Overfull \hbox (2139.42662pt too wide) in paragraph at lines 53--54 +[]\OML/cmm/m/it/10 robabilistic[]\OT1/cmr/m/n/10 014\OML/cmm/m/it/10 ; whichwew +illcallChIPPartitioning; isreallyinteresting:ChIPPartitioningisaprobabilisticpa +rtitioningmethodthatsoftlyclustersasetsofgenomicregionsbasedontheirsignalshape\ +OT1/cmr/m/n/10 (\OML/cmm/m/it/10 asopposedtotheabsolutevalues\OT1/cmr/m/n/10 )\ +OML/cmm/m/it/10 resemblance:Toensurepropercomparisonsbetweentheregions; thealgo +rithmallowstooffsetoneregioncomparetotheothertoretrieveasimilarsignalatdifferen +toffsetsandtoflipthesignalorientation:Finally; ithasbeendemonstratedtobereallyr +obusttosparsedata:$ + [] + +Missing character: There is no T in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no x in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no P in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no q in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! 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+Missing character: There is no s in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no x in font nullfont! 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Undefined control sequence. + ...ference `atac_seq_em' on page \thepage + \space undefined\on@line . +l.59 ...re is depicted in Figure \ref{atac_seq_em} + A. +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). 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Undefined control sequence. + ...ference `atac_seq_em' on page \thepage + \space undefined\on@line . +l.61 ...As illustrated in Figure \ref{atac_seq_em} + , this procedure is actual... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + + +LaTeX Warning: Reference `atac_seq_em' on page undefined on input line 61. + +Missing character: There is no , in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no . in font nullfont! + +Overfull \hbox (20.0pt too wide) in paragraph at lines 61--62 +[] + [] + + +Overfull \hbox (10.86105pt too wide) in paragraph at lines 61--62 +[] + [] + +! Undefined control sequence. +l.64 \subsection + {Data realignment} +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +Missing character: There is no D in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! + +Overfull \hbox (20.0pt too wide) in paragraph at lines 64--65 +[] + [] + +Missing character: There is no A in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no A in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no F in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +! Undefined control sequence. + ...ference `atac_seq_em' on page \thepage + \space undefined\on@line . +l.66 ...As illustrated in Figure \ref{atac_seq_em} + , this procedure is actual... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + + +LaTeX Warning: Reference `atac_seq_em' on page undefined on input line 66. + +Missing character: There is no , in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no . in font nullfont! + +Overfull \hbox (20.0pt too wide) in paragraph at lines 66--67 +[] + [] + + +Overfull \hbox (10.86105pt too wide) in paragraph at lines 66--67 +[] + [] + +Missing character: There is no I in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no x in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no M in font nullfont! +Missing character: There is no N in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no - in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no q in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no C in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no I in font nullfont! +Missing character: There is no P in font nullfont! +Missing character: There is no P in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no q in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! 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+Missing character: There is no . in font nullfont! + +Overfull \hbox (20.0pt too wide) in paragraph at lines 72--73 +[] + [] + +! Undefined control sequence. +l.75 \section + {Nucleosome organization around transcription factor binding si... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +Missing character: There is no N in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no z in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! + +Overfull \hbox (20.0pt too wide) in paragraph at lines 75--76 +[] + [] + + +! LaTeX Error: Environment figure undefined. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.78 \begin{figure} + +Your command was ignored. +Type I to replace it with another command, +or to continue without it. + + +Overfull \hbox (20.0pt too wide) in paragraph at lines 79--79 +[] + [] + +! Undefined control sequence. +l.80 \includegraphics + [scale=0.25]{images/ch_encode_peaks/MNase_profiles.png... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +Missing character: There is no [ in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no = in font nullfont! +Missing character: There is no 0 in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no 2 in font nullfont! +Missing character: There is no 5 in font nullfont! +Missing character: There is no ] in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no / in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +! Missing $ inserted. + + $ +l.80 \includegraphics[scale=0.25]{images/ch_ + encode_peaks/MNase_profiles.png... +I've inserted a begin-math/end-math symbol since I think +you left one out. Proceed, with fingers crossed. + +! Extra }, or forgotten $. +l.80 ...es/ch_encode_peaks/MNase_profiles.png.png} + +I've deleted a group-closing symbol because it seems to be +spurious, as in `$x}$'. But perhaps the } is legitimate and +you forgot something else, as in `\hbox{$x}'. In such cases +the way to recover is to insert both the forgotten and the +deleted material, e.g., by typing `I$}'. + +! Undefined control sequence. +l.81 \captionof + {figure}{\textbf{TODO} TODO.} +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + + +! LaTeX Error: Command \end{center} invalid in math mode. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.83 \end{center} + +Try typing to proceed. +If that doesn't work, type X to quit. + + +! LaTeX Error: Something's wrong--perhaps a missing \item. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.83 \end{center} + +Try typing to proceed. +If that doesn't work, type X to quit. + + +! LaTeX Error: Something's wrong--perhaps a missing \item. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.83 \end{center} + +Try typing to proceed. +If that doesn't work, type X to quit. + +! Missing $ inserted. + + $ +l.83 \end{center} + +I've inserted something that you may have forgotten. +(See the above.) +With luck, this will get me unwedged. But if you +really didn't forget anything, try typing `2' now; then +my insertion and my current dilemma will both disappear. + +! Missing } inserted. + + } +l.83 \end{center} + +I've inserted something that you may have forgotten. +(See the above.) +With luck, this will get me unwedged. But if you +really didn't forget anything, try typing `2' now; then +my insertion and my current dilemma will both disappear. + + +! LaTeX Error: \begin{document} ended by \end{figure}. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.84 \end{figure} + +Your command was ignored. +Type I to replace it with another command, +or to continue without it. + + +Overfull \hbox (265.3679pt too wide) in paragraph at lines 80--85 +[]\OML/cmm/m/it/10 ncode[]eaks=MNase[]rofiles:png:png[][][]$ + [] + +Missing character: There is no F in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! 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+! 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+Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no F in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no k in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no M in font nullfont! +Missing character: There is no N in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no - in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no q in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no C in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no I in font nullfont! +Missing character: There is no P in font nullfont! +Missing character: There is no P in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no B in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no q in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no C in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no I in font nullfont! +Missing character: There is no P in font nullfont! +Missing character: There is no P in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no 1 in font nullfont! +Missing character: There is no 5 in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no ( in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no - in font nullfont! +Missing character: There is no 7 in font nullfont! +Missing character: There is no 0 in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no - in font nullfont! +Missing character: There is no 1 in font nullfont! +Missing character: There is no 0 in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no 0 in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no + in font nullfont! +Missing character: There is no 1 in font nullfont! +Missing character: There is no 0 in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no + in font nullfont! +Missing character: There is no 7 in font nullfont! +Missing character: There is no 0 in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no ) in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no A in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! +Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! Missing character: There is no c in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no i in font nullfont! +Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! -Missing character: There is no i in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! -Missing character: There is no i in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no q in font nullfont! -Missing character: There is no u in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no F in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no c in font nullfont! +Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! -Missing character: There is no l in font nullfont! +Missing character: There is no s in font nullfont! 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Undefined control sequence. + ...de_peaks_em_examples' on page \thepage + \space undefined\on@line . +l.88 ...igure \ref{suppl_encode_peaks_em_examples} + ). Additionally, it was al... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + + +LaTeX Warning: Reference `suppl_encode_peaks_em_examples' on page undefined on + input line 88. + +Missing character: There is no ) in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no A in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! 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Missing character: There is no n in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! -Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! +Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no y in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no q in font nullfont! -Missing character: There is no u in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! -Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no f in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no f in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no p in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no k in font nullfont! -Missing character: There is no w in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! -Missing character: There is no d in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! -Missing character: There is no . in font nullfont! -Missing character: There is no T in font nullfont! -Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no b in font nullfont! -Missing character: There is no u in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no w in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no d in font nullfont! +Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no ' in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no k in font nullfont! -Missing character: There is no n in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no p in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no x in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no y in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no . in font nullfont! -Missing character: There is no T in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no u in font nullfont! -Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no g in font nullfont! +Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no g in font nullfont! Missing character: There is no i in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! -Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! +Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no p in font nullfont! +Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no k in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no - in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! +Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! +Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no - in font nullfont! -Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! -Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no u in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no z in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Missing character: There is no C in font nullfont! + +Overfull \hbox (20.0pt too wide) in paragraph at lines 88--89 +[] + [] + + +Overfull \hbox (10.86105pt too wide) in paragraph at lines 88--89 +[] + [] + +Missing character: There is no I in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no m in font nullfont! -Missing character: There is no p in font nullfont! -Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no g in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no w in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no x in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no i in font nullfont! +Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no s in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! -Missing character: There is no h in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no m in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no i in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no x in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! Missing character: There is no n in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! +Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no F in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! -Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no I in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! -Missing character: There is no p in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! -Missing character: There is no l in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! -Missing character: There is no . in font nullfont! -Missing character: There is no S in font nullfont! +Missing character: There is no d in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no , in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no i in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no y in font nullfont! +! Undefined control sequence. +l.90 ... array density measure developed by \citep + {zhang_canonical_2014}. A ... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +Missing character: There is no z in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no s in font nullfont! +Missing character: There is no g in font nullfont! +! Missing $ inserted. + + $ +l.90 ...density measure developed by \citep{zhang_ + canonical_2014}. A class p... +I've inserted a begin-math/end-math symbol since I think +you left one out. Proceed, with fingers crossed. + +! Extra }, or forgotten $. +l.90 ... developed by \citep{zhang_canonical_2014} + . A class pattern showing ... +I've deleted a group-closing symbol because it seems to be +spurious, as in `$x}$'. But perhaps the } is legitimate and +you forgot something else, as in `\hbox{$x}'. In such cases +the way to recover is to insert both the forgotten and the +deleted material, e.g., by typing `I$}'. + +! Missing $ inserted. + + $ +l.91 + +I've inserted a begin-math/end-math symbol since I think +you left one out. Proceed, with fingers crossed. + + +Overfull \hbox (20.0pt too wide) in paragraph at lines 90--91 +[] + [] + + +Overfull \hbox (3873.23946pt too wide) in paragraph at lines 90--91 +[]\OML/cmm/m/it/10 anonical[]\OT1/cmr/m/n/10 014\OML/cmm/m/it/10 :Aclasspattern +showingwellpositionednucleosomesistypicallyshowingsharpregionsofstrongsignalsep +aratedbysignaldepletedregionsreflectingofthealternanceofnucleosomepresence=abse +nce:ThemethoddevelopedbyZhangandcolleaguesbasicallysearchesforstrongvariationso +fsignal:Thehighestthescore; themostthepatterncontainstowellpositionednucleosome +s:Ontheotherhand; theabilityofaTFtoactasananchorforarraysorganizationwasmeasure +dasthestandarddeviationoftheshiftusedbyChIPPartitioning:Briefly; itispossibleto +computetheprobabilitydensityoftheusageofeachshiftstate:Assessinghowmuchthediffe +rentshiftstateswereusedisindicativeofhowmuchtheindividualpatternswerealignedatt +hebeginning:Astandarddeviationvaluewouldindicatethattheshiftingtendstobethesame +forallbindingsitesandthusthatthenucleosomearraysoccuratafixed \OMS/cmsy/m/n/10 +^^@ + [] + + +Overfull \hbox (60.93095pt too wide) in paragraph at lines 90--91 +\OML/cmm/m/it/10 unspecified \OMS/cmsy/m/n/10 ^^@ + [] + + +Overfull \hbox (349.28513pt too wide) in paragraph at lines 90--91 +\OML/cmm/m/it/10 distancefromthebindingsite:Inthiscase; thebindingsitecouldbeth +earrayanchor:$ + [] + +! Undefined control sequence. +l.95 \section + {The case of CTCF, ZNF143, YY1, SMC3 and RAD21} +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +Missing character: There is no T in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! -Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no a in font nullfont! Missing character: There is no f in font nullfont! -Missing character: There is no u in font nullfont! +Missing character: There is no C in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no C in font nullfont! +Missing character: There is no F in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no Z in font nullfont! +Missing character: There is no N in font nullfont! +Missing character: There is no F in font nullfont! +Missing character: There is no 1 in font nullfont! +Missing character: There is no 4 in font nullfont! +Missing character: There is no 3 in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no Y in font nullfont! +Missing character: There is no Y in font nullfont! +Missing character: There is no 1 in font nullfont! +Missing character: There is no , in font nullfont! +Missing character: There is no S in font nullfont! +Missing character: There is no M in font nullfont! +Missing character: There is no C in font nullfont! +Missing character: There is no 3 in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no c in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no R in font nullfont! +Missing character: There is no A in font nullfont! +Missing character: There is no D in font nullfont! +Missing character: There is no 2 in font nullfont! +Missing character: There is no 1 in font nullfont! + +Overfull \hbox (20.0pt too wide) in paragraph at lines 95--96 +[] + [] + +! Undefined control sequence. +l.98 \section + {Study of CTCF interactor motifs} +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +Missing character: There is no S in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no i in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no C in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no C in font nullfont! +Missing character: There is no F in font nullfont! +Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no s in font nullfont! + +Overfull \hbox (20.0pt too wide) in paragraph at lines 98--99 +[] + [] + +! Undefined control sequence. +l.101 \section + {The EBF1 case} +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +Missing character: There is no T in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no E in font nullfont! +Missing character: There is no B in font nullfont! +Missing character: There is no F in font nullfont! +Missing character: There is no 1 in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! + +Overfull \hbox (20.0pt too wide) in paragraph at lines 101--102 +[] + [] + +! Undefined control sequence. +l.104 \section + {Methods} +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +Missing character: There is no M in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no s in font nullfont! + +Overfull \hbox (20.0pt too wide) in paragraph at lines 104--105 +[] + [] + +! Undefined control sequence. +l.106 \subsection + {Data and data processing} +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +Missing character: There is no D in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no . in font nullfont! -Missing character: There is no F in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no i in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no s in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no n in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no , in font nullfont! -Missing character: There is no T in font nullfont! -Missing character: There is no F in font nullfont! -Missing character: There is no b in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no d in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! + +Overfull \hbox (20.0pt too wide) in paragraph at lines 106--107 +[] + [] + +Missing character: There is no A in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no G in font nullfont! +Missing character: There is no M in font nullfont! +Missing character: There is no 1 in font nullfont! +Missing character: There is no 2 in font nullfont! +Missing character: There is no 8 in font nullfont! +Missing character: There is no 7 in font nullfont! +Missing character: There is no 8 in font nullfont! +Missing character: There is no E in font nullfont! +Missing character: There is no N in font nullfont! +Missing character: There is no C in font nullfont! +Missing character: There is no O in font nullfont! +Missing character: There is no D in font nullfont! +Missing character: There is no E in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! -Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no m in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no v in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! +Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no u in font nullfont! -Missing character: There is no p in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no r in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no 1 in font nullfont! +Missing character: There is no 9 in font nullfont! +Missing character: There is no g in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no o in font nullfont! Missing character: There is no m in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! +Missing character: There is no c in font nullfont! Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no w in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no M in font nullfont! +Missing character: There is no G in font nullfont! +Missing character: There is no A in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no m in font nullfont! -Missing character: There is no w in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no y in font nullfont! +! Undefined control sequence. +l.108 ...can be found on the MGA repository \citep + {dreos_mga_2018}. +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +Missing character: There is no d in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! Missing character: There is no s in font nullfont! -Missing character: There is no p in font nullfont! +! Missing $ inserted. + + $ +l.108 ...found on the MGA repository \citep{dreos_ + mga_2018}. +I've inserted a begin-math/end-math symbol since I think +you left one out. Proceed, with fingers crossed. + +! Extra }, or forgotten $. +l.108 ...the MGA repository \citep{dreos_mga_2018} + . +I've deleted a group-closing symbol because it seems to be +spurious, as in `$x}$'. But perhaps the } is legitimate and +you forgot something else, as in `\hbox{$x}'. In such cases +the way to recover is to insert both the forgotten and the +deleted material, e.g., by typing `I$}'. + +! Missing $ inserted. + + $ +l.109 + +I've inserted a begin-math/end-math symbol since I think +you left one out. Proceed, with fingers crossed. + + +Overfull \hbox (20.0pt too wide) in paragraph at lines 108--109 +[] + [] + + +Overfull \hbox (40.27443pt too wide) in paragraph at lines 108--109 +[]\OML/cmm/m/it/10 ga[]\OT1/cmr/m/n/10 018\OML/cmm/m/it/10 :$ + [] + +Missing character: There is no P in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no k in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no c in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no o in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no y in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no b in font nullfont! +Missing character: There is no E in font nullfont! +Missing character: There is no N in font nullfont! +Missing character: There is no C in font nullfont! +Missing character: There is no O in font nullfont! +Missing character: There is no D in font nullfont! +Missing character: There is no E in font nullfont! +Missing character: There is no C in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no u in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no q in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! Missing character: There is no u in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no c in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no . in font nullfont! -Missing character: There is no O in font nullfont! +Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no t in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no p in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no o in font nullfont! +Missing character: There is no i in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no r in font nullfont! Missing character: There is no l in font nullfont! -Missing character: There is no y in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no [ in font nullfont! +\citation{gerstein_architecture_2012} +! Undefined control sequence. + ...: Citation `\@citeb ' on page \thepage + \space undefined\on@line . +l.110 ...ipeline \cite{gerstein_architecture_2012} + were used. These peaks ca... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + + +LaTeX Warning: Citation `gerstein_architecture_2012' on page undefined on inpu +t line 110. + +Missing character: There is no ] in font nullfont! +Missing character: There is no w in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! +Missing character: There is no u in font nullfont! Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! +Missing character: There is no k in font nullfont! Missing character: There is no s in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no r in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no q in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no o in font nullfont! Missing character: There is no u in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +! Undefined control sequence. +l.110 ...re used. These peaks can be found at \url + {https://ccg.epfl.ch/mga/h... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +Missing character: There is no h in font nullfont! +Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no p in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no o in font nullfont! Missing character: There is no p in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no : in font nullfont! +Missing character: There is no / in font nullfont! +Missing character: There is no / in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no . in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no r in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! -Missing character: There is no y in font nullfont! +Missing character: There is no . in font nullfont! Missing character: There is no c in font nullfont! -Missing character: There is no o in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no / in font nullfont! Missing character: There is no m in font nullfont! -Missing character: There is no p in font nullfont! +Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no t in font nullfont! +Missing character: There is no / in font nullfont! Missing character: There is no h in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no 1 in font nullfont! +Missing character: There is no 9 in font nullfont! +Missing character: There is no / in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! -Missing character: There is no h in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no / in font nullfont! +Missing character: There is no U in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no - in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no F in font nullfont! +Missing character: There is no B in font nullfont! +Missing character: There is no S in font nullfont! +Missing character: There is no / in font nullfont! +Missing character: There is no U in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! Missing character: There is no m in font nullfont! -Missing character: There is no a in font nullfont! +Missing character: There is no - in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no F in font nullfont! +Missing character: There is no B in font nullfont! +Missing character: There is no S in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no A in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no r in font nullfont! Missing character: There is no g in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no z in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no F in font nullfont! +Missing character: There is no b in font nullfont! Missing character: There is no i in font nullfont! -Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! +Missing character: There is no D in font nullfont! +Missing character: There is no N in font nullfont! +Missing character: There is no A in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no u in font nullfont! Missing character: There is no g in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! +Missing character: There is no g in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no . in font nullfont! -Missing character: There is no F in font nullfont! Missing character: There is no i in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no n in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no v in font nullfont! +Missing character: There is no k in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! +Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no m in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no r in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no g in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! Missing character: There is no i in font nullfont! +Missing character: There is no z in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no y in font nullfont! -Missing character: There is no b in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! 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The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -Missing character: There is no h in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -! Missing $ inserted. - - $ -l.17 ...t decade. Dedicated algorithms \citep{hon_ - chromasig:_2008} \citep{ni... -I've inserted a begin-math/end-math symbol since I think -you left one out. Proceed, with fingers crossed. -! Extra }, or forgotten $. -l.17 ...ted algorithms \citep{hon_chromasig:_2008} - \citep{nielsen_catchprofi... -I've deleted a group-closing symbol because it seems to be -spurious, as in `$x}$'. But perhaps the } is legitimate and -you forgot something else, as in `\hbox{$x}'. 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Undefined control sequence. -l.17 ...orithms \citep{hon_chromasig:_2008} \citep - {nielsen_catchprofiles:_20... + ...: Citation `\@citeb ' on page \thepage + \space undefined\on@line . +l.110 ...OCO v10 \cite{kulakovskiy_hocomoco:_2016} + or Jolma \cite{jolma_dna-... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -! Undefined control sequence. -l.17 ...\citep{nielsen_catchprofiles:_2012} \citep - {kundaje_ubiquitous_2012} ... -The control sequence at the end of the top line -of your error message was never \def'ed. If you have -misspelled it (e.g., `\hobx'), type `I' and the correct -spelling (e.g., `I\hbox'). Otherwise just continue, -and I'll forget about whatever was undefined. -! Undefined control sequence. -l.17 ...12} \citep{kundaje_ubiquitous_2012} \citep - {nair_probabilistic_2014} ... -The control sequence at the end of the top line -of your error message was never \def'ed. If you have -misspelled it (e.g., `\hobx'), type `I' and the correct -spelling (e.g., `I\hbox'). Otherwise just continue, -and I'll forget about whatever was undefined. +LaTeX Warning: Citation `kulakovskiy_hocomoco:_2016' on page undefined on inpu +t line 110. +Missing character: There is no ] in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no J in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no [ in font nullfont! +\citation{jolma_dna-binding_2013} ! Undefined control sequence. -l.17 ...12} \citep{nair_probabilistic_2014} \citep - {groux_spar-k:_2019} have ... + ...: Citation `\@citeb ' on page \thepage + \space undefined\on@line . +l.110 ...6} or Jolma \cite{jolma_dna-binding_2013} + collection. Using the cor... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -! Missing $ inserted. - - $ -l.18 - -I've inserted a begin-math/end-math symbol since I think -you left one out. 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Undefined control sequence. -l.22 ...robabilistic algorithm developed by \citep - {nair_probabilistic_2014},... -The control sequence at the end of the top line -of your error message was never \def'ed. If you have -misspelled it (e.g., `\hobx'), type `I' and the correct -spelling (e.g., `I\hbox'). Otherwise just continue, -and I'll forget about whatever was undefined. - -Missing character: There is no n in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! -! Missing $ inserted. - - $ -l.22 ...listic algorithm developed by \citep{nair_ - probabilistic_2014}, which... -I've inserted a begin-math/end-math symbol since I think -you left one out. Proceed, with fingers crossed. - -! Extra }, or forgotten $. -l.22 ...veloped by \citep{nair_probabilistic_2014} - , which we will call ChIPP... -I've deleted a group-closing symbol because it seems to be -spurious, as in `$x}$'. But perhaps the } is legitimate and -you forgot something else, as in `\hbox{$x}'. In such cases -the way to recover is to insert both the forgotten and the -deleted material, e.g., by typing `I$}'. - -! Missing $ inserted. - - $ -l.23 - -I've inserted a begin-math/end-math symbol since I think -you left one out. Proceed, with fingers crossed. - - -Overfull \hbox (20.0pt too wide) in paragraph at lines 22--23 -[] - [] - - -Overfull \hbox (2139.42662pt too wide) in paragraph at lines 22--23 -[]\OML/cmm/m/it/10 robabilistic[]\OT1/cmr/m/n/10 014\OML/cmm/m/it/10 ; whichwew -illcallChIPPartitioning; isreallyinteresting:ChIPPartitioningisaprobabilisticpa -rtitioningmethodthatsoftlyclustersasetsofgenomicregionsbasedontheirsignalshape\ -OT1/cmr/m/n/10 (\OML/cmm/m/it/10 asopposedtotheabsolutevalues\OT1/cmr/m/n/10 )\ -OML/cmm/m/it/10 resemblance:Toensurepropercomparisonsbetweentheregions; thealgo -rithmallowstooffsetoneregioncomparetotheothertoretrieveasimilarsignalatdifferen -toffsetsandtoflipthesignalorientation:Finally; ithasbeendemonstratedtobereallyr -obusttosparsedata:$ - [] - - -! LaTeX Error: Missing \begin{document}. - -See the LaTeX manual or LaTeX Companion for explanation. -Type H for immediate help. - ... - -l.24 T - his algorithm models the signal over a region of length $L$ has having... - -You're in trouble here. Try typing to proceed. -If that doesn't work, type X to quit. - -Missing character: There is no T in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no i in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no g in font nullfont! +Missing character: There is no p in font nullfont! 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Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no g in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no x in font nullfont! -Missing character: There is no p in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no t in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no t in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no - in font nullfont! -Missing character: There is no m in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no x in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no m in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no z in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no ( in font nullfont! -Missing character: There is no E in font nullfont! -Missing character: There is no M in font nullfont! -Missing character: There is no ) in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no m in font nullfont! -Missing character: There is no e in font nullfont! Missing character: There is no w in font nullfont! -Missing character: There is no o in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! -Missing character: There is no k in font nullfont! -Missing character: There is no . in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no y in font nullfont! Missing character: There is no G in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no v in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! +Missing character: There is no [ in font nullfont! +\citation{gaffney_controls_2012} +! Undefined control sequence. + ...: Citation `\@citeb ' on page \thepage + \space undefined\on@line . +l.112 ...d colleagues \cite{gaffney_controls_2012} + and can be found at \url{... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + + +LaTeX Warning: Citation `gaffney_controls_2012' on page undefined on input lin +e 112. + +Missing character: There is no ] in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! -Missing character: There is no m in font nullfont! Missing character: There is no o in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no , in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! +! Undefined control sequence. +l.112 ...y_controls_2012} and can be found at \url + {https://ccg.epfl.ch/mga/h... +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + Missing character: There is no h in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no : in font nullfont! +Missing character: There is no / in font nullfont! +Missing character: There is no / in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no . in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no f in font nullfont! Missing character: There is no l in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no k in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no i in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no / in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no c in font nullfont! +Missing character: There is no / in font nullfont! Missing character: There is no h in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no e in font nullfont! Missing character: There is no g in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! +Missing character: There is no 1 in font nullfont! +Missing character: There is no 9 in font nullfont! +Missing character: There is no / in font nullfont! Missing character: There is no g in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no v in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no f in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no 1 in font nullfont! +Missing character: There is no 2 in font nullfont! +Missing character: There is no / in font nullfont! +Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no c in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no 1 in font nullfont! +Missing character: There is no 2 in font nullfont! +Missing character: There is no . in font nullfont! Missing character: There is no h in font nullfont! -Missing character: There is no c in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no m in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no c in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no m in font nullfont! -Missing character: There is no p in font nullfont! -Missing character: There is no u in font nullfont! Missing character: There is no t in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! -Missing character: There is no . in font nullfont! -Missing character: There is no A in font nullfont! -Missing character: There is no p in font nullfont! -Missing character: There is no o in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no i in font nullfont! +Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no p in font nullfont! -Missing character: There is no r in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no b in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no b in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no l in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no y in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no f in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no c in font nullfont! Missing character: There is no l in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no a in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no v in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no h in font nullfont! Missing character: There is no r in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no c in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no p in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no u in font nullfont! Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no - in font nullfont! +Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no , in font nullfont! -Missing character: There is no b in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no m in font nullfont! -Missing character: There is no p in font nullfont! +Missing character: There is no q in font nullfont! Missing character: There is no u in font nullfont! -Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no p in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no b in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no b in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no i in font nullfont! -Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! -Missing character: There is no c in font nullfont! +Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no n in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no t in font nullfont! +Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no p in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no " in font nullfont! +Missing character: There is no A in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no P in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no t in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no - in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! -Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no c in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no p in font nullfont! Missing character: There is no l in font nullfont! -Missing character: There is no u in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no . in font nullfont! -Missing character: There is no T in font nullfont! -Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no - in font nullfont! +Missing character: There is no 1 in font nullfont! +Missing character: There is no 4 in font nullfont! +Missing character: There is no 7 in font nullfont! +Missing character: There is no b in font nullfont! 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Missing character: There is no g in font nullfont! +Missing character: There is no D in font nullfont! +Missing character: There is no N in font nullfont! Missing character: There is no a in font nullfont! -Missing character: There is no w in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no t in font nullfont! +Missing character: There is no I in font nullfont! +Missing character: There is no - in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no q in font nullfont! Missing character: There is no d in font nullfont! 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Emergency stop. <*> ch_encode_peaks.tex *** (job aborted, no legal \end found) Here is how much of TeX's memory you used: - 11 strings out of 492982 - 232 string characters out of 6134895 - 57262 words of memory out of 5000000 - 3676 multiletter control sequences out of 15000+600000 + 25 strings out of 492982 + 606 string characters out of 6134895 + 64262 words of memory out of 5000000 + 3690 multiletter control sequences out of 15000+600000 3948 words of font info for 15 fonts, out of 8000000 for 9000 1141 hyphenation exceptions out of 8191 - 18i,2n,14p,1096b,94s stack positions out of 5000i,500n,10000p,200000b,80000s + 18i,5n,21p,1435b,123s stack positions out of 5000i,500n,10000p,200000b,80000s ! ==> Fatal error occurred, no output PDF file produced! diff --git a/main/ch_encode_peaks.tex b/main/ch_encode_peaks.tex index 8630c30..6fde53b 100644 --- a/main/ch_encode_peaks.tex +++ b/main/ch_encode_peaks.tex @@ -1,72 +1,118 @@ \cleardoublepage \chapter{ENCODE peaks analysis} \markboth{ENCODE peaks analysis}{ENCODE peaks analysis} \addcontentsline{toc}{chapter}{ENCODE peaks analysis} Modeling a TF sequence specificity only allows to partially understand how a TF binds a region. Indeed, scanning a genome using a PWM for putative binding sites often returns tens of thousands of sites with only a subset of them being really occupied within a cell. Other elements such as chromatin organization and composition are likely to drive TF binding. Thus gaining a better understanding about the chromat It is now clear that nucleosome occupancy fulfils more than a packaging role. It can also acts as a barrier to impede DNA reading processes and compete with TFs for sequence occupancy.% The exact mechanisms at play remain unclear but nucleosome occupancy is thought to shelter DNA sequence - as some bases are facing the core octamer or to distort the DNA structure - impeding sequence recognition by TFs. In vivo, evidences for competition between TFs and nucleosomes have been collected. Computational simulations accounting for simultaneous multiple factor binding on DNA suggested that nucleosome occupancy and TFs binding influence each other and that TF binds nucleosome depleted regions \cite{wasson_ensemble_2009}. As discussed above, the organization of chromatin has a deep impact on TF binding. Nucleosomes and TFs are in competition to bind DNA. Because TFs are ultimate forces driving gene expression, understanding how chromatin influence them, or at least how chromatin is organized around them, is crucial. \section{Data} % number of peaks per dataset \begin{figure} \begin{center} \includegraphics[scale=0.3]{images/ch_encode_peaks/peaklist_peaknumber_GM12878.png} \captionof{figure}{\textbf{Number of peaks in GM12878} called by ENCODE for each TF ChIP-seq experiment. The different TFs are colored by type, as defined by \citep{cheng_understanding_2012} : sequence specific TF (TFSS), non specific TF (TFNS), chromatin structure (ChromStr), chromatin modifier (ChromModif), RNAPII associated factors (Pol2), RNAPIII associated factors (Pol3) and others. The horizontal dashed lines indicate 20'000 and 40'000.} \label{encode_peaks_gm12878_peak_number} \end{center} \end{figure} % proportion of peaks with motif per dataset \begin{figure} \begin{center} \includegraphics[scale=0.3]{images/ch_encode_peaks/peaklist_proportions_GM12878.png} \captionof{figure}{\textbf{Proportion of peaks with a motif in GM12878}, for each TF ChIP-seq experiment, in green. Assuming that a TF binds to DNA through its motif, the motif should be nearby the peak center. Thus the center of each peak was scanned using a PWM describing the TF binding specificity. Each TF was associated to a log-odd PWM contained either in JASPAR Core vertebrate 2014 \citep{mathelier_jaspar_2014}, HOCOMOCO v10 \citep{kulakovskiy_hocomoco:_2016} or Jolma \citep{jolma_dna-binding_2013} collection. If a motif instance with a score corresponding to a pvalue higher or equal to $1\cdot10^{-4}$ could be found, the peak was considered bearing a motif. The different TFs are colored by type, as defined by \citep{cheng_understanding_2012} : sequence specific TF (TFSS), non specific TF (TFNS), chromatin structure (ChromStr), chromatin modifier (ChromModif), RNAPII associated factors (Pol2), RNAPIII associated factors (Pol3) and others.} \label{encode_peaks_gm12878_motif_prop} \end{center} \end{figure} In an effort to better understand how the genome is organized and how its functions are fulfilled, the ENCODE Consortium which released an impressive collection of coherent data representing an un- precented picture of the chromatin in human cell lines. The GM12878 cells were choosen as one of the highest priority cell line. GM12878 are widely-used lymphoblastoids. Because of their ability to divide and of their normal karyotype - unlike HeLa cells - these cells are a good model for genomic studies. In these cells, the ENCODE Consortium released ChIP-seq data 53 different TFs. Additionally, nucleosome occupancy (MNase-seq) and chromatin accessiblity (DNasI-seq) data were generated with a depth of coverage. Furthermore, the ENCODE Consortium also released peaks called using their uniform processing pipeline \cite{gerstein_architecture_2012}. These peaks are interesting because i) they are called from technical replicate ChIP-seq samples and ii) several peak callers are used and the different results are integrated. Because of this, these peaks can be considered as an excellent standard. As expected, the number of peaks called for each TF was highly variable and likely reflects each factor activity in this cell line \ref{encode_peaks_gm12878_peak_number}. The most abundant factor in terms of peaks was RUNX3 followed by CTCF. This observation fits to BioGPS \citep{wu_biogps:_2016} data which indicates that both RUNX3 and CTCF are highly expressed in lymphoblast and in B cells compared to other tissues. Regarding CTCF, it is involved in chromatin looping [REFERENCE] by forming homodimers. This has potential multiply by 2 the number of peaks. Moreover, the propensity of each TF to bind through their motifs was also variable, with again CTCF being showing the highest values \ref{encode_peaks_gm12878_motif_prop}. \section{ChIPPartitioning : an algorithm to identify chromatin architectures} Discovering over-represented chromatin architectures over a set of regions of interest - let's say containing a TF binding site in their middle - is a long standing problem in bioinformatics. More formerly, given a matrix $R$ of dimensions $NxL$ containing $N$ vectors of read counts $r_{1}, r_{2}, ..., r_{N}$ of length $L$, each containing the number of reads mapping at a given position in a given region, find $K \leq N$ vectors of length $L' \leq L$ that contain over-represented signals found in the $N$ regions of $R$. This can actually be solved using clustering methods which groups regions that look alike into $K$ groups. The summary of the signal inside each group - for instance the mean signal for the K-means algorithm - can then be interpreted as the over-represented chromatin architectures. Because of the technical limitations of the sequencing library preparation protocols, two major issues should be faced. First, the $N$ regions of interest are usually aligned with respect to a feature of interest, for instance a TF binding site. TF binding sites are usually identified by calling peaks on ChIP-seq data. TF binding sites identified using ChIP-seq peaks come with a positional uncertainty that is equal to half of the peak width. The binding site is inside but we don't know exactly where. Thus aligning the regions using the peak center - for instance - does not guarantee to align the binding sites. Comparing two regions chromatin organization then necessitate to first realign them properly. Second, the regions can show a functional orientation. For instance, TF binding sites have an upstream and a downstream with respect to the bound sequence. Orienting properly the regions is also required to properly compare the chromatin organizations in two regions. Finally, the signal over some regions may be sparse because of a sub-optimal sequencing depth. The study of signal distribution over genomic regions has been a quite active field for bulk sequencing experiments during the last decade. Dedicated algorithms \citep{hon_chromasig:_2008} \citep{nielsen_catchprofiles:_2012} \citep{kundaje_ubiquitous_2012} \citep{nair_probabilistic_2014} \citep{groux_spar-k:_2019} have been developed to cluster genomic regions based on their distribution of reads, which reflects their function. - % The major issue faced where i) to assess whether two regions had the same signal, they had to be properly aligned, ii) even if the regions were properly aligned, they had to be properly oriented and iii) the signal may be sparse due to an sub-optimal sequencing depth. Most of these algorithms and softwares deal with some of these issues cited above. However, the probabilistic algorithm developed by \citep{nair_probabilistic_2014}, which we will call ChIPPartitioning, is really interesting. ChIPPartitioning is a probabilistic partitioning method that softly clusters a sets of genomic regions based on their signal shape (as opposed to the absolute values) resemblance. To ensure proper comparisons between the regions, the algorithm allows to offset one region compare to the other to retrieve a similar signal at different offsets and to flip the signal orientation. Finally, it has been demonstrated to be really robust to sparse data. This algorithm models the signal over a region of length $L$ has having being sampled from a mixture of $K$ signal models, using $L$ independent Poisson distributions. The number of reads sequenced over this region is then the result of this sampling process. The entire set of regions is assumed to have been generated from a mixture of $K$ different signal models (classes). Each class is represented by a vector of $L' \leq L$ values that represent the expected number of reads at each position for that class. These values are thus the Poisson distribution parameters. In order to discover the $K$ different chromatin signatures in the data, the algorithm proceed to a maximum likelihood estimation of the Poisson distribution parameters using an expectation-maximization (EM) framework. Given a set of $K$ models, the likelihoods of each region given each class is computed. A posterior probability of each class given each region can, in turn, be computed. These probabilities can be interpreted as a soft clustering. The parameters of the classes are updated using a weighted aggregation of the signal. Since each region is computed a probability to belong to each class, it participates to the update of all the classes, with different weights. If the length of the chromatin signature searched $L'