Constitutive exons & constitutively spliced introns

[hsu yuming]

Hi all,

I’m interested in comparing alternative splicing (AS) in exons of orthologous genes, specifically in cases where AS events are detected in one species but not in another. I would like to know if there is data produced by rMATs that quantifies JC reads for constitutive exons or introns.

Currently, I have used the --statoff option in rMATs 4.12 to separately identify AS events in samples from two species. I found some SE events with a PSI of 1 and RI events with a PSI of 0. Below are examples from SE.MATS.JC.txt and RI.MATS.JC.txt that can be defined as constitutive exons and constitutively spliced introns.

The case of SE

The case of RI

It appears that using --statoff can produce constitutive features in [AS].MATS.JC.txt. I’d like to confirm if this file consistently contains all constitutive annotated exons or only features under certain scenarios. If not all constitutive exons and constitutively spliced introns are reported, what are the criteria for the cases that I found to be reported?

Additionally, are there intermediate files where I can find JC counts for exons identified as constitutive, or are these discarded at some point?

Thanks a lot.

Yu-Ming

[kutsc...@gmail.com]

rMATS will only detect an event if there is evidence for all exons and splice junctions in the event. The evidence can be from either the reads (like --b1) or the --gtf. In the example you show for the SE event, SJC_SAMPLE_1 is 0,0,0,0. In that case the support for the skipping junction has to be from the --gtf. Here's a post about rMATS event detection: https://github.com/Xinglab/rmats-turbo/issues/161#issuecomment-974119283

If you want to get rMATS output for certain exons or introns you can add transcripts to the --gtf. Another option is to write the fromGTF.[AS].txt files yourself and then use --fixed-event-set

This post describes the format of the intermediate .rmats files: https://github.com/Xinglab/rmats-turbo/issues/363

The .rmats files have read counts that are used to calculate the JC counts for detected events. You may be able to extract the information you're interested in from those files

Eric