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Old 02-27-2014, 01:26 PM   #14
Location: Australia, Brisbane

Join Date: Nov 2012
Posts: 13

Hi Simon,

sorry for that. I'm still a beginner in this field and i'm still learning how all this works.
The thread on bioconductor list is more focused on DESeq2 analysis than htseq-count but I was indeed going to provide the link to this thread since the discussion was shifting towards htseq-count again.

Did you have a chance to read my previous post?

I think the issue I'm having (other than having the correct design for DESeq2) is that there are particular loci in the genome that have overlapping genes on the same strand. Though, these genes have a different ID so that's way I get a count of 0 .

As explaind in htseq manual If a read maps to an exon shared by several genes, this will appear to htseq-count as ambigous.

So at the moment I am having zero counts for all these particular loci, which sometimes contain also really highly expressed genes that I'd like to account for in the subsequent DGE analysis.

Do you have any idea on how I could account for this?

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