question regarding p-value for each intron usage

[seyoun209]

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]

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.