Hi all-
I've been searching high and low but can't find a good answer to this. To clarify up front, I'm not asking about differences in GC content between samples. I'm wondering about GC bias within a particular transcript. A gene I'm interested in has an overall GC content of around 70% but one half of the gene is about 50% while the other half sits at around 80%. When I look at my mapped reads, almost all the reads mapping to that gene end up in the half that is around 50% GC with none of the reads mapping to the 80% GC end. As a result, the gene doesn't appear to be highly expressed in my dataset, even though I know that it is (measured by qPCR).
Talking with some colleagues, it appears this is relatively common. Is there any way to account for this in my analysis pipeline? It seems like most of the tools available are to correct GC bias between samples, but I can't find anything about correcting or accounting for within transcript GC disparity.
Thanks!
