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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The immune system’s power comes from its genetic diversity, allowing myriad threats to be neutralized through first recognizing foreign antigens. That diversity is also what makes the immune system so difficult to study. Recent advances in sequencing technology and computational biology, however, are giving researchers new tools to understand immune responses and immune-related diseases in greater detail.
This convergence of genetics, immunology, and computation...09-01-2026, 05:41 AM
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