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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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question regarding p-value for each intron usage #238

Open seyoun209 opened 1 year ago

seyoun209 commented 1 year ago

Dear Leafcutter team,

I am curious that I am trying to get the p-value for each intron usage, not the clu level. My only thought was getting t-test between comparison of ratio or counts (control vs. case) but any ideas?

TimD1 commented 10 hours ago

Leafcutter's prepare_results.R script outputs an RData file that contains a matrix counts of per-junction coverage counts. Using this matrix and countdata's bb.test module, we were able to obtain p-values for each junction.