Meaning of IncLevel for A3SS/A5SS events

[Peili]

Hello,

a quick question on IncLevel1/IncLevel2 for A3SS and A5SS events in MATS_output:

is the IncLevel for the inclusion of the short exon or the long exon? for instance, one line from A5SS.MATS.JunctionCountOnly.txt

longExonStart_0base longExonEnd shortES shortEE flankingES  flankingEE  ID  IJC_SAMPLE_1    SJC_SAMPLE_1    IJC_SAMPLE_2    SJC_SAMPLE_2    IncFormLen  SkipFormLen PValue  FDR IncLevel1   IncLevel2   IncLevelDifference

41878989    41879289    41878989    41879175    41879534    41879719    36147   2162,2429   655,704 5295,5178   330,407 237 124 3.93018950717e-14   6.02163985341e-11   0.633,0.644 0.894,0.869 -0.243

my sample_1 has lower incLevel of this event. does sample_1 have less of the long upstream exon or the short one?

I haven't been able to find any documentation or user group discussion to help me understand. hope this is an easy documentation-type question that you will spare 1 minute to give me the answer.

Best Regards,

peili

[YI XING]

For both alt5ss and alt3ss, the inclusion isoform is the long exon form. You can find the illustration in Fig. S1 of the rMATS paper (http://www.pnas.org/content/111/51/E5593.full.pdf?with-ds=yes)

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[X L]

Hi, Peril,

I have the same issue. I haven't found a place in the documentation to give me details of the meaning of "short ES" and "short EE" in the A3SS event type.

Xiao

[kutsc...@gmail.com]

The labeled coordinates for the events are shown in this post: https://github.com/Xinglab/rmats-turbo/issues/158#issuecomment-966763718

There is a description in the README: https://github.com/Xinglab/rmats-turbo/tree/v4.3.0?tab=readme-ov-file#output
> The inclusion form includes the long exon (longExonStart_0base, longExonEnd) instead of the short exon (shortES shortEE)

Eric

[X L]

Hi, Eric,

Thank you very much! The image in the post is very illustrative!

Xiao