[BioC] Rsamtools - summarizeOverlaps - count read on complementary strand

Devon Ryan dpryan at dpryan.com
Fri Apr 18 10:29:59 CEST 2014

Just swap the strand in your GRanges object and then use ignore.strand=FALSE with summarizeOverlaps. Something like:

strand(gr) <- ifelse(strand(gr)=="+", "-", "+")

That will work unless you have features without strands, at least.


Devon Ryan, Ph.D.
Email: dpryan at dpryan.com
Molecular and Cellular Cognition Lab
German Centre for Neurodegenerative Diseases (DZNE)
Ludwig-Erhard-Allee 2
53175 Bonn, Germany

On Apr 18, 2014, at 10:01 AM, samuel collombet [guest] wrote:

> Hi!
> I have RNAseq data which are single-end (50b), strand specific, but reads are the complement of the RNA (ie reads are always on the complementary strand to their corresponding gene). 
> I would like to count reads on genes using summarizeOverlaps, however I do not find the way to tell him to count reads that are on the complementary strand to the exons. Is there a way? (with HTseq-count, I was using the option --stranded=reverse).
> -- output of sessionInfo(): 
> none
> --
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