How IsoQuant works when multiple samples are given as input?

[dslv3y]

Hi,
I have a question about how IsoQuant handles multiple samples. From my understanding, it processes each input file separately (rather than pooling them together) but still assigns the same names to identical isoforms across samples by using a single constructed database for the entire run. Is this correct?

I may have missed this detail in the documentation, so I would appreciate any clarification. Thank you for your time!

[andrewprzh]

Dear @dslv3y

I think this might not be mentioned in documentation, only in the paper.
For the transcript discovery (I guess you implied this part) IsoQuant does combine all the files together and constructs a single annotation for all samples. Further, it estimates the counts for each sample individual.

Just in case, the first part, i.e. reference based analysis, is done independently for each sample.

Best
Andrey

[dslv3y]

Dear @andrewprzh

Thank you for clarifying! Yes, I was referring to the transcript discovery part. I really appreciate you providing this information so swiftly.

Best,
Dmitry