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davidaknowles / leafcutter

Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
http://davidaknowles.github.io/leafcutter/
Apache License 2.0
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How can I get PSI for sample-level? #89

Closed zhengjiantao closed 5 years ago

zhengjiantao commented 5 years ago

I have already finished step 2: define intron clustering and I want to get the PSI for per sample? How can I don that? Thanks advanced!

davidaknowles commented 5 years ago

This isn't something that leafcutter usually outputs on the basis it would be pretty noisy. We do however use it for the sQTL analysis so you can use the script described here: http://davidaknowles.github.io/leafcutter/articles/sQTL.html Note you may not want to remove any PCs if you just want to look at the raw ratios.