HI All,
I am interested in allele specific expression in bumblebee genes. I have over twenty RNA-seq libraries. Using Quasar (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393517/pdf/btu802.pdf) I found 555 loci showing allele specific expression in at least three libraries. Preprint is available here if anyone is interested (http://biorxiv.org/content/early/2017/01/23/022657).
The problem:
A reviewer pointed out that with just RNA-seq I cannot rule out adenosine to inosine gene editing. They suggested I check the SNP conversions and indeed there is a preponderance of A->G and C->T (although weirdly, there is also a lot of G->A and T->C). Is there a standard way to deal with this? Numerous methods have been developed to look at ASE with genotyping, but none as far as I can see mention the adenosine to inosine problem.
One possible solution would be to identify RNA editing and then remove it from my data. But the method I found to do it (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676881/pdf/nihms469411.pdf) is basically assume common conversions not in a database are RNA editing. I don't think this is very useful here.
Any help would be much appreciated.
Take care
Eamonn
