CoverageBed for RNA-seq strand-specific and paired-end data
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6.8 years ago

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

RNA-Seq • 1.9k views
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Entering edit mode
6.8 years ago

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.

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