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Old 02-27-2014, 04:19 AM   #11
Location: Australia, Brisbane

Join Date: Nov 2012
Posts: 13

Hi Simon,

I might have figured this out.

I think the issue is that I have 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 .

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.

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

Let me know if I'm not clear

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