Computing Normalized Counts For Exons In Edger

Question

[Nick]

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?

Answer 1

[Devon Ryan]

You can't derive exon-level metrics from gene-level metrics. DEXSeq comes with some scripts meant to count reads mapping to exonic bins, so just use that. I suspect that featureCounts can do this as well, but have never tried.