[BioC] Computing normalized counts for exons in edgeR

Ryan rct at thompsonclan.org
Sun Mar 30 08:21:41 CEST 2014

There is no way to derive exon-level counts from gene-level counts. You 
will have to go back to the bam files and perform a separate counting 
step for exons.

On Sat Mar 29 17:48:02 2014, 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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