Result interpretation

[elva0328]

hello, rmats2sashimiplot is a wonderful tool. I've already got the result, but I'm confused about how to interpret the result, could you help with this.
for example:

in this skipped exon event, we have samples 1-3, which sample has the SE event? or which sample has the increased SE event? and what additional information we can see from the result?
appreciate your response.

[EricKutschera]

All three samples "have the event" since there are reads that skip the exon and also reads that include the exon in each sample. Sample 1 has the lowest inclusion level (IncLevel: 0.31) so you could say that it shows an increase in the frequency of exon skipping compared to the other samples

This sashimiplot shows that there are no junction reads going from the left exon to the middle exon, but there are skipping junctions (96 in sample 1) and junctions going from the middle exon to the right exon (86 in sample 1). Ideally you would see similar numbers for the left junction and the right junction like in the plots from the rmats2sashimiplot README: https://github.com/Xinglab/rmats2sashimiplot/tree/v2.0.4

[elva0328]

thanks very much, Eric. but I still have one question, for skipped exon event, the samples with lower lncLevel show an increase in the frequency. how about for the other 4 splicing events, can we use the same standard to identify the samples with increase splicing eVent. such as the sample with lower lncLevel show an increase in the frequency of RI, MXE, A3SS,A5SS?

[EricKutschera]

https://github.com/Xinglab/rmats-turbo/tree/v4.1.1#output has a diagram which shows the definitions of inclusion isoforms and skipping isoforms for each event type (SE, A5SS, ...). The README also has some additional notes about the definition of the inclusion isoforms:

SE: The inclusion form includes the target exon (exonStart_0base, exonEnd)
MXE: If the strand is + then the inclusion form includes the 1st exon (1stExonStart_0base, 1stExonEnd) and skips the 2nd exon. If the strand is - then the inclusion form includes the 2nd exon (2ndExonStart_0base, 2ndExonEnd) and skips the 1st exon
A3SS, A5SS: The inclusion form includes the long exon (longExonStart_0base, longExonEnd) instead of the short exon (shortES shortEE)
RI: The inclusion form includes (retains) the intron (upstreamEE, downstreamES)

For SE (skipped exon) events, lower inclusion level means more of the skipping isoform which skips the exon and matches up with the name of the event. For RI (retained intron) events, higher inclusion level means more of the inclusion isoform which retains the intron and matches up with the name of the event. For the other event types (MXE, A3SS, A5SS), the name of the event does not indicate one isoform over the other

[elva0328]

@EricKutschera thanks very much. it helps me a lot!