search

mritchielab / FLAMES

A framework for performing single-cell and bulk read full-length analysis of mutations and splicing.
https://mritchielab.github.io/FLAMES/
GNU General Public License v3.0
17 stars 9 forks source link

Integrate Bambu results for multiple samples #38

Open koehlek99 opened 2 months ago

koehlek99 commented 2 months ago

Hi, thanks a lot for developing this tool!

I ran the develop version using Bambu for transcript identification. I feel like I read somewhere that the multisample run for Bambu is not implemented yet, so I ran it separately on each sample.

Do you have a suggestion how to compare the novel transcripts and merge counts between samples? Do the Bambu IDs match or should I collapse them somehow?

Thanks a lot in advance!

Best, Krissi

ChangqingW commented 2 months ago

Hmm, I did wrote not yet implemented for multi-sample. They do have a multi-sample mode. I'll try to hook it up with it.

ChangqingW commented 2 months ago

There is gffcompare to merge similar transcripts. If you do not merge similar ones, I guess your novel transcripts might be very sample-specific, e.g. when there is a genuine shared novel transcript across samples it might get called slightly differently in each sample.