CoverageBed for RNA-seq strand-specific and paired-end data

Question

[anaritagrosso]

Hi,

I would like to obtain the read coverage from a bam file containing RNA-seq strand-specific and paired-end data. The coveragebed tool can not distinguish the strand-specific information from paired-end data (i.e. only consider the forward or reverse read strand information).

Anyone has a suggestion to easily obtain the coverage?

Thank you

Ana Rita Grosso

Answer 1

[Alastair Kerr]

The Deeptools package is useful for this, specifically the bamCoverage program within it. It has useful documentation using the "--help" flag but I think the "--filterRNAstrand" option will be what you are looking for.