Allele specific expression (ASE) using unfiltered reads from RNA-seq data?

Question

[mbk0asis]

Hi, all!

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.

Thank you!

[Matteo Schiavinato]

Can you edit the message commenting on what you mean with filtered reads in this context? Trimmed adapters, deduplicated, quality filtering, all of them?