Integrate Bambu results for multiple samples

[koehlek99]

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]

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]

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.