Hi,

I have questions for the rMATS output files. I have tried to find the novel events by using --novelSS, which gives the fromGTF.novelSpliceSite.[AS_Event].txt file and the file I focus on would be the [AS_Event].MATS.JC.txt one.

However, what I'm wondering is that I know that rMATS gives the results of both novel and annotated events, is the file [AS_Event].MATS.JC.txt contains both novel and annotated events results?

If it's true, is it possible to separate the novel and annotated events results in [AS_Event].MATS.JC.txt file?