Hi I am interested in ways I can quantify and potentially bin + vs - strand mapping in my PE data from Bowtie2? Seeing some variability in which stand the read mapped to across the genome and wanted to look at it more. thanks
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To count the number of reads mapped on the forward strand:
samtools view -c -F20 sample.bam
and on the reverse:
samtools view -c -f16 -F4 sample.bam
Just omit the -c if you want to extract the reads (add -b to output in BAM format rather than SAM).
There are lots more possibilities for filtering on SAM flags. This site is useful to help understand what the different flag codes mean mean:
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