Question: CoverageBed for RNA-seq strand-specific and paired-end data
gravatar for anaritagrosso
3.2 years ago by
anaritagrosso0 wrote:


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

rna-seq • 1.2k views
ADD COMMENTlink modified 22 months ago by Biostar ♦♦ 20 • written 3.2 years ago by anaritagrosso0
gravatar for Alastair Kerr
3.2 years ago by
Alastair Kerr5.3k
Manchester/UK/Cancer Biomarker Centre at CRUK-MI
Alastair Kerr5.3k wrote:

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.

ADD COMMENTlink written 3.2 years ago by Alastair Kerr5.3k
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