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Zero output for sel.rn=rowSums(cnts) != 0

Hi, I get a problem when I want to try step 2 from "RNA-seq data pathway and gene-set analysis workflow" by Weijun Luo. I get zero rows with value !=0.

> p.cnts=assay(gnCnt)
> cnts=p.cnts
> dim(cnts)
[1] 7017    2
> sel.rn=rowSums(cnts) !=0
> cnts=cnts[sel.rn,]
> dim(cnts)
[1] 0 2

I have discussed it in another thread also, if you need more information. Any advise?

rowsums summarizeoverlaps
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updated by Ram Ram • written by Parham Parham

1 answer

I answered in a comment elsewhere, but the base of the problem ended up being that Parham has single-end data but was telling summarizeOverlaps(), which was used to produce gnCnt, to only use paired-end reads.

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written by Devon Ryan Devon Ryan

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