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TheFraserLab / ASEr

Get ASE counts from BAMs or raw fastq data -- repackage of pipeline by Carlo Artieri
MIT License
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Incorporating quality scores for ASE counts #18

Open rmagoglia opened 8 years ago

rmagoglia commented 8 years ago

Curious what others think about this - when we find a read overlapping a SNP and we can match it to its parent of origin, should we be checking the quality score of that base in the read (and have it pass a certain quality threshold) before counting that read towards the total counts for that parental allele? To me this seems more in keeping with other methods (e.g. mpileup) and might yield more reliable results.

petercombs commented 8 years ago

I think that's a reasonable idea, and it wouldn't even be that hard to implement. I am skeptical that it would necessarily change a whole lot, since my understanding is that the vast majority of Illumina bases are of very high quality . Unless you have a some evidence pointing towards a lot of reads getting mis-categorized, I don't think it's worth your time.

tehranchi commented 8 years ago

Yep, that's what I do. It won't change "a lot" percentage wise but it will likely have an effect on the false positives regarding ASE calls.

On Nov 10, 2016, at 2:53 PM, Peter Combs notifications@github.com wrote:

I think that's a reasonable idea, and it wouldn't even be that hard to implement. I am skeptical that it would necessarily change a whole lot, since my understanding is that the vast majority of Illumina bases are of very high quality . Unless you have a some evidence pointing towards a lot of reads getting mis-categorized, I don't think it's worth your time.

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