check https://broadinstitute.github.io/picard/explain-flags.html to choose a proper flag
multiBamSummary
Hi
I want to count reads in defined intervals using multiBamSummary from deepTools. I want to count reads only on the reverse strand. Will --samFlagInclude 16 work? And when I want to count reads on the forward strand will --samFlagExclude 16 work ?
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