fromGTF.AS_Event.txt and JCEC vs. JC

[flynn...@yale.edu]

Dear rMATS User Group,

Thankfully, I was able to debug some command line argument issues from a previous post, and get some results. However, I was wondering what do these output files represent, especially fromGTF.AS_Event.txt. Are these fromGTF.AS_Event.txt files only generated from the GTF file (or one or both RNA bam files)? I ask this question because I noticed that if I ran rMATS with different bam sample files but same annotation file, I would obtain fromGTF.AS_Event.txt files of different number of lines (content). Would these GTF files have a set of same underlying alternative events if a union was taken for these GTF files derived from different bam samples?

Also, if we want to obtain just the exon inclusion rate from one sample, what is the difference between the inclusion rate in JCEC and JC? What is the significance of differentiating between JCEC and JC?

Thank you in advance for your time for answering my questions. This group has been incredibly helpful for using this software.

Best,

Flynn

[Shihao Shen]

HI Flynn,

Thanks for your interest in rMATS.

The fromGTF.AS_Event.txt files include both events from annotation and novel splicing events detected by the reads from bam files.

JCEC uses both junction reads and reads covered only on the targeted exon in its calculation. JC only uses junction reads. We found that these two are mostly consistent. It is a user choice to use either one, although JCEC uses more reads in its calculation.

Thanks,

Shihao