ccmeth

When the load process was not successful, I could not close R studio normally and need to quit with "force". I noticed that although R studio was closed, after checking...

I directly downloaded the .hic files from Rao et al., 2014 Cell with GSE63525. > Must have something to do with that non-round number in the last entry, the second...

> do you know which specific .hic file is throwing this error? It can be related to some chrs in some cell lines with normalization (KR) not converging so bias...

> should be fixed now. Let me know how it goes. Thanks for providing such a useful tool! So based on the above communication, the mustache installed via pip3 does...

Aha..... I think reinstall isoquant with v3.5.0 will address this issue, since visualize.py does not use scr package installed via pip.

> Hi @ccmeth - just checking in to see if you resolved your issue? While visualization.py was implemented in version 3.5, we have added functionality to process Isoquant runs from...

> HI @ccmeth I see, thank you for the context. ".params" is a file (pickle serialization) we generate that captures all your parameters. Would you mind sending your isoquant.log? Thanks!...

> hi @ccmeth I have opened up a PR that will address this issue! I know Andrey is OOO at the moment, so the changes are on the find_genes branch...

> hi @ccmeth I have opened up a PR that will address this issue! I know Andrey is OOO at the moment, so the changes are on the find_genes branch...

Another question is related to read_assignments.tsv. I read the instructions and realized that column "assignment events" should correspond to "isofrom_id". For instance, contents of column "assignment events", "ism_3,fake_terminal_exon_5:24892-29320", indicated two...