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metatran_LBE/20200821_mapping_on_features_d427_hybridAB.sh
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20200821_mapping_on_features_d427_hybridAB.sh
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#create index
bowtie2-build -f /media/bioinfoteam/SCRATCH_850GB/databases/assembly_hybridAB/d427AB_annotation.ffn /media/bioinfoteam/SCRATCH_850GB/databases/assembly_hybridAB_annotation
bowtie2 --local -x /media/bioinfoteam/SCRATCH_850GB/databases/assembly_hybridAB_annotation -X 5000 --very-sensitive-local -k 50 -p 4 --phred33 -1 /media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/rRNA_sorting/non-aligned/31C_L1_non_aligned_R1.fastq -2 /media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/rRNA_sorting/non-aligned/31C_L1_non_aligned_R2.fastq -S /media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/bowtie_output/31C_map_on_d427_hybridAB_annotation.sam
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