Andrey Prjibelski

@rebeelouise Unfortunately, I am the only one currently working on IsoQuant. It's very hard to predict current timeline considering other ongoing research projects. I really hope I can get my...

Dear @Kyung-TaeLee Thank you for the feedback! Yes, I work on our own barcode calling and UMI deduplication. In brief, it is currently in `sc_v3` branch. It can be run...

Dear @qsonehara You are right, in this file X corresponds to terminal exons according to the provided annotation. So, a terminal exon is spanned by a read that, for example,...

Dear @qsonehara Thanks a lot for bringing this up. I kinda thought about this when I posted my reply. I will try to implement the new way of counting exons...

Should be fixed in 3.7

Dear @Seongmin-Jang-1165 Your ran failed due to the operating system limit on the number of open files, which can be changed using ulimit -n I presume setting something like 10000...

Please, reopen if needed.

@sparthib Yes, SQANTI-like output contains only information about novel transcripts. Could send me a example? It would also be nice to see both novel and assigned known transcripts from the...

@sparthib I agree, headers would be nice. I'll add them in the next release. I think I used information from [SQANTI wiki](https://github.com/ConesaLab/SQANTI3/wiki/Understanding-the-output-of-SQANTI3-QC#classifcols), but it might have changed over time.. Moreover,...

@sparthib I think I found the reason for the original problem with FSM records. IsoQuant outputs a few novel isoforms that are very similar to the reference ones, which should...