EduEyras
commented
4 years ago Hola Alejandro,
Thanks for your message. Unfortunately not. But this is on purpose, to make SUPPA independent of read counts and the specifics of the read mapping. SUPPA works only with the transcript abundances, regardless of where they come from. This makes it faster and simpler.
We've made before comparisons of PSIs from SUPPA with those from the junction counts, calculated e.g. with sjcount, or rMATS. If you use SUPPA with quantification from methods like Salmon, at low expression the Salmon assignments sometimes don't agree with the BAMs from say, STAR, and that leads to some discrepancies. A way to have a better correspondence is to estimate TPMs with Salmon using BAMs from Star.
I don't know if that's what you want, but I hope it helps
best
Eduardo
On Mon, 26 Oct 2020 at 20:12, Alejandro Reyes notifications@github.com wrote:
Hi SUPPA developers,
Thanks for your the continuous development of SUPPA. Apologies if I miss this in the documentation, but is it possible to retreive the event-level counts per junction from SUPPA2?
For instance, for a SE event, is it possible to get the raw counts for e1-s2, e2-s3 and e1-s3 in each sample?
Best regards, Alejandro
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/comprna/SUPPA/issues/106, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKBZTFEZJ64ZI5EX3QM3SMU4PZANCNFSM4S7DHC6A .
-- 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
areyesq89
Hi SUPPA developers,
Thanks for your the continuous development of SUPPA. Apologies if I miss this in the documentation, but is it possible to retreive the event-level counts per junction from SUPPA2?
For instance, for a SE event, is it possible to get the raw counts for e1-s2, e2-s3 and e1-s3 in each sample?
Best regards, Alejandro