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Allele specific expression (ASE) using unfiltered reads from RNA-seq data?
Entering edit mode
13 months ago
mbk0asis • 420
Korea, Republic Of

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!

Entering edit mode

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


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