I'm trying to measure the allele specific expression (ASE) levels of selected genes from RNA-seq data.
My question is if it's OK to use unfiltered read counts to calculate the ASE.
As I understand, GATK does various statistical(?) tests, which I can't understand, to filter out bad reads and determine genotypes.
Thus, to calculate the ASE, I think something similar steps should be included.
I found number of tools for ASE, but I'm curious how bad the results would be if I use the unfiltered reads.
Sorry for such a vague question. I just want to hear what people think.