EricKutschera
commented
4 months ago rMATS-long doesn't output a PSI value. Instead it outputs transcript abundance and transcript proportion within a gene. Then it describes the differences between pairs of transcripts in terms of splicing events. Having the transcript counts might be enough in many cases, but a PSI value could still be useful. For SE events you could maybe use the ratio of transcript abundance from transcripts that include the exon to transcripts which have the skipping junction. You could also count exons and junctions directly from the alignment file
The script that detects alternative splicing events will not report an event based on transcript endpoints: https://github.com/Xinglab/rMATS-long/blob/v1.0.0/scripts/FindAltTSEvents.py#L173
In that example it looks like the difference is the 3' endpoint of the transcript and not an A3SS of an internal exon
kwonej0617
Hello @EricKutschera
Thank you for developing such a useful tool. I was wondering whether or not there's a way to get PSI value from this tool. Is it not necessary to have PSI values when studying AS events using long-read seq data (nanopore) because it generates full-length transcript information?
In addition, I have a question regarding the output of rMATS-long. Here is my data from rMATS-long.
The result below describes there is SE event between ENST00000259021.9 and ENST00000424009.6 isoforms. However, when I checked the structure figure, it seems to have exon skipping and alternative 3 splice site events. I wonder if rMATS-long determines multiple alternative splicing event as well.
Looking forward to hearing from you.
Thank you!