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brentp / goleft

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
MIT License
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crai resolution in output-indexcov.bed.gz #77

Closed corinsexton closed 2 months ago

corinsexton commented 2 months ago

Hi there,

I'm running indexcov on around 2,000 crai files and I had a quick question about the resolution within the output-indexcov.bed.gz file. I see that the windows are the standard 16,384bp that are used for bam indices. Is this the expected behavior for indexcov when using cram indices as well?

Thanks!

brentp commented 2 months ago

hi, yes this is expected. It interpolates to the same window size even though the cram index resolution is different and often much lower.

corinsexton commented 2 months ago

Got it. So in your experience would it be appropriate to filter out low quality samples based on the bin counts generated from crai files? Or is that too much of a stretch with the low resolution?

brentp commented 2 months ago

It's hard to make a blanket statement, but usually if you look at the html output and there are outliers, it's worth looking into those further.

corinsexton commented 2 months ago

That makes sense. Thanks for all the clarifications!