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

Question

[Parham]

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?

[Parham]

I have a link to the BAM files I used for this analysis here now, if someone can kindly look it up and see if something is wrong with them.

https://drive.google.com/folderview?id=0Bxl0rZon0OuzQUNuQzVoUDlnNXM&usp=sharing

Thanks!

Answer 1

[Devon Ryan]

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.