How IsoQuant label novel isoform discovery in the OUT.transcript_models.gtf

[yuntianf]

Hi,
Thanks for the great tool.
I'm using IsoQuant to process my data and I want to check if there exist any new isoforms.
According to the documentation I checked the OUT.transcript_models.gtf, but within the gtf anntation I only find canonical isoforms.
For the novel isoform, how would they be labeled in that gtf?

Thanks!

[andrewprzh]

Dear @yuntianf

The transcript ids containing "nic" and "nnic" are novel isoforms (novel in catalog and novel not in catalog respectively).
Canonical property only refers to splice sites being canonical.

Best
Andrey