Question: Rsamtools - summarizeOverlaps - count read on complementary strand
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5.4 years ago by
Guest User12k
Guest User12k 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 -- Sent via the guest posting facility at bioconductor.org.
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ADD COMMENTlink modified 5.4 years ago by Devon Ryan200 • written 5.4 years ago by Guest User12k
Answer: Rsamtools - summarizeOverlaps - count read on complementary strand
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gravatar for Devon Ryan
5.4 years ago by
Devon Ryan200
Germany
Devon Ryan200 wrote:
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 ____________________________________________ 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 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 5.4 years ago by Devon Ryan200
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