Michael Hiller

Hi all, sorry, I was on vacation when this was discussed. Thx ReverendCasy for explaining all. Here is a supplement figure that visually explains the intact RF measures 

UCSC's kent source provides gtfToBed and gff3ToBed. This has worked for us well in the past.

Hi, 1) your stats plot shows that almost all genes are classified as missing. I assume this is because the chains you use are very incomplete. 2) Yes, extracting lost...

Hi, ~50000 will likely refer to transcripts we annotate in the query. Not genes. Most genes have several transcripts. And some transcripts have several orthologous loci (called projections). We often...

Is this the only transcript that fails? And if you run this single job in isolation, is the error repeatable? @kirilenkobm Could you pls have a look? The error message...

OK, it looks like everything works for many transcript but the Mctp2 one crashes. I have never seen this error before unfortunately. @kirilenkobm Could you pls have a look? Have...

Hi, sorry, if we were not able to fix the TOGA1 problem you describe. We are now releasing TOGA2 for beta-testing https://github.com/hillerlab/TOGA2 TOGA2 is much faster and 300X less memory-demanding....

Hi, sorry, if we were not able to fix the TOGA1 problem you describe. We are now releasing TOGA2 for beta-testing https://github.com/hillerlab/TOGA2 TOGA2 is much faster and 300X less memory-demanding....

Hi Dong-Ha, this size limitation could be a problem. I think we tweaked a limit in the kent src code on our system to allow for larger single chroms. If...

Thx for sending the files. All works on my side (log below; I didn't specify all the optional parameters, but they will not matter for the crash on your side)....