About summary.txt

[mshn15]

Hello Mr EricKutschera.
Thank you very much for developing this useful tool. I have a few questions about the result output summary.txt file.
1.The data included in the file, SigEventsJCHigherInclusion, can I understand that in the SE type, the larger this value, the fewer the number of skipping events that occur in the corresponding sample?
2.At the same time, I would like to ask if it is possible to generate data similar to SigEventsJCHigherInclusion, but for HigherExclusion?

Thanks for your response！

[EricKutschera]

This is the code for the columns like SigEventsJCSample1HigherInclusion:
https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/rMATS_P/summary.py#L88

It's checking whether IncLevelDifference is positive or negative and from https://github.com/Xinglab/rmats-turbo/tree/v4.3.0?tab=readme-ov-file#output

IncLevelDifference: average(IncLevel1) - average(IncLevel2)

SigEventsJCSample1HigherInclusion is the number of events where sample 1 had a higher inclusion level than sample 2 for that event. The inclusion level is a ratio describing how much read support there is for the inclusion isoform compared to the skipping isoform. Even if one sample group has a higher inclusion level than the other, the event can still occur in both sample groups

Here are some related posts:
Xinglab/rmats2sashimiplot#68
#175 (comment)
#257 (comment)