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Bishop-Laboratory / RLPipes

RLPipes: A standardized R-loop-mapping pipeline.
https://anaconda.org/bioconda/rlpipes
MIT License
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Need rules for spikein data #71

Open millerh1 opened 2 years ago

millerh1 commented 2 years ago

We need rules that can handle spikein data sets (e.g., qDRIP) and appropriately normalize coverage and counts tables

pbousquets commented 2 years ago

Hi! The implementation of this feature is something you have in mind on the short-term? I was about to use your pipeline, but my data has spike-ins and I wanted to make use of that during the normalization.

millerh1 commented 2 years ago

Hi @pbousquets thank you for your interest in RLPipes. That is a high priority feature. However, I simply haven't had the time yet to implement it. If you want to submit a PR, that would be very welcome!

pbousquets commented 2 years ago

Great @millerh1! Is there any approach you as creators had in mind?

millerh1 commented 2 years ago

I think something simple would be to calculate the scale factor (maybe using an approach like this) and then supply it to bamCoverage in deepTools to normalize bigWig files. We haven't implemented any tools yet for dealing with read count tables, so I think just the bigWig normalization would be required for now.