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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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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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