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metatran_LBE/20200820_SAM_to_BAM.sh
b4a73f19d755mapping_withrRNA

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20200820_SAM_to_BAM.sh
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conda activate samtools_env
export WORKING_DIR=/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/bowtie_output
cd $WORKING_DIR
###################################################### convert SAM into BAM file ######################################################
for filename in $(ls *'.sam')
do
#echo $filename
fileID=`expr match "$filename" '\([0-9]*C_map_on_d427_hybridAB\)'`
#echo $fileID
export OUTPUT=/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/bowtie_output/SAMTools/${fileID}_sort
#convert file
samtools view -S -b $filename > $fileID.bam
#check conversion
samtools view $fileID.bam | head
done
###################################################### Sort alignments by name ######################################################
for filename in $(ls *'.sam')
do
#echo $filename
fileID=`expr match "$filename" '\([0-9]*C_map_on_d427_hybridAB\)'`
#echo $fileID
export OUTPUT=/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/bowtie_output/SAMTools/${fileID}_sort
samtools sort -o $OUTPUT.sam -n $filename
done
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