Hi all, I'm looking at exon quantification from RNAseq data and for a given gene the quantification for each exon varies to other exons. I'm trying to understand what the reason behind this difference is. I guess some of it can be explained by different transcripts, so if an exon is not present in transcript A then the quantification of that exon compared to the others which are present across all transcripts will be lower. But this is the only reason I can come up with, ignoring that I'd expect the exon quantification to be quite similar across the gene.
Are there any other reasons why some exons appear to be more expressed than others? I've tried looking this up but haven't found anything, any references or thoughts/ideas are very appreciated.
Thank you
GC bias can play a role. The salmon quantification tool implements the suggested method from the video in its
--gcBiasflag. Still, differences in uniqueness and mappability will do their part into making exon coverage everything than equal across the same gene.