multiBamSummary

Question

[Hina]

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 ?

Answer 1

[JC]

Yes, --samFlagExclude 16 will exclude reads in the reverse strand, you need --samFlagInclude 16 (primary hits, reverse strand) or some combination for the flags

[JC]

check https://broadinstitute.github.io/picard/explain-flags.html to choose a proper flag