[BioC] Computing normalized counts for exons in edgeR

Wei Shi shi at wehi.EDU.AU
Mon Mar 31 00:36:22 CEST 2014

I don't think you can get exon-level counts from a gene-level analysis because your read counts were already summarized for genes.

To get normalized counts for exons, you need to get raw counts for exons first. To do this, you can use the featureCounts command in Rsubread package.


featureCounts accepts GTF annotation as input. You should set useMetaFeatures=FALSE and allowMultiOverlap=TRUE when you try to get read counts for exons.

Note that featureCounts can get you read counts for genes as well.

Hope this helps.


On Mar 30, 2014, at 11:48 AM, Nick N wrote:

> I've done standard rna-seq differential expression analysis on a gene level
> using edgeR. For downstream analysis I would like to extract the normalized
> counts for a particular exon. What is the best way to go about it? Can I
> derive the normalized counts for that exon straight from my analysis (e.g.
> by using, say, cpm())?
> The first workaround that pops to my mind is that I could simply edit
> either the GTF or the raw count data to discard any counts for other exons
> of that gene, than simply run the standard count normalisation and I would
> get the normalized counts for that exon masquerading as the normalized
> count for the corresponding gene. But this seems too hacky and dirty
> solution. Can anyone give advice on how to do this properly?
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