Hi Xiaojia, MISO doesn't do novel isoform detection, only quantitates isoforms based on the annotation it is fed, as you noted. One thing some of our users have done is to run a de-novo isoform assembly program (or use some other means to compile an annotation with novel isoforms), convert these de novo isoforms into events in GFF3 format, and run MISO on the resulting annotation to get isoform expression.
Yarden > On Jun 26, 2016, at 5:36 PM, Tang, Xiaojia, Ph.D. <[email protected]> > wrote: > > Hi everyone on the miso ML, > > I have been using MISO for identifying possible alternative splicing events > in RNA-Seq data. It works well for events that are in the GFF3 files. > However, this time in a new analysis we are expected to detect some > exon-skipped events in a known isoform, which would result in a novel > isoform. We have been able to see it happen in IGV. But we will need to use > some algorithm in order to detect such events genome-widely. I know that > MISO’s event-centric or isoform-centric model would work basing on the > provided events, and also only detected those events/isoforms. Is there a way > to detect possible skipping events of a known exon which might be a novel > event resulting in a novel isoform? > > Thanks, > Xiaojia > Informatics Specialist > Department of Health Sciences Research > Mayo Clinic Rochester > Rochester, MN 55901 > > _______________________________________________ > miso-users mailing list > [email protected] > http://mailman.mit.edu/mailman/listinfo/miso-users _______________________________________________ miso-users mailing list [email protected] http://mailman.mit.edu/mailman/listinfo/miso-users
