EduEyras
commented
3 years ago Hi,
sorry there is not more information available.
The strict format of RI events in SUPPA is very strict because it requires external exonic boundaries to be the same in all isoforms including/excluding the intron. So having this more relaxed definition of retained introns is a good case scenario for his option.
With the variable option, you would measure whether an intron is retained, regardless of what's happening outside the intron region.
With SE events it is something similar. With the variable option, the PSI is mainly capturing the inclusion of the exon, even if there are junctions to multiple different flanking exons.
This translates to how events and PSIs are measured using RT-PCR-based techniques. Sometimes the PCR primers cannot be specific to a flanking exon and may capture more than one exon from the flank, hence collecting more transcripts contributing to the inclusion or the skipping. In those cases, the PSIs from SUPPA would correlate better with the PSIs from RT-PCR
We have seen this to be relevant in some species where genes have genes with many alternative transcripts that have short introns and multiple overlapping events, like in Arabidopsis thaliana.
I hope this is informative. I'll be happy to give you more details if necessary
best
Eduardo
On Mon, 24 May 2021 at 10:11, tonyaseverson @.***> wrote:
One of the options mentioned in the repo is -b V to allow variable event boundaries. I've been looking through Alamancos et al. and Trincado et al. and the SUPPA2 repo, but unless I've missed something, I do not see any description of when its use might be desirable (or caveats concerning its application). All primary literature that I've found so far in which SUPPA2 has been used seems to use the default (strict) option.
Use appears to dramatically alter the relative abundance of RI, A3 and A5 events, and almost doubles the number of events identified. Could you provide some information about its intended use case(s)?
Thanks!
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-- Prof. E Eyras EMBL Australia Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ
tonyaseverson
One of the options mentioned in the repo is -b V to allow variable event boundaries. I've been looking through Alamancos et al. and Trincado et al. and the SUPPA2 repo, but unless I've missed something, I do not see any description of when its use might be desirable (or caveats concerning its application). All primary literature that I've found so far in which SUPPA2 has been used seems to use the default (strict) option.
Use appears to dramatically alter the relative abundance of RI, A3 and A5 events, and almost doubles the number of events identified. Could you provide some information about its intended use case(s)?
Thanks!