Dylan Kotliar

Hi. Yep, I fixed it by manually appending gene_name and transcript_name entries to the rows that were missing them in the GTF. I simply used the gene_id and transcript_id for...

Sure! I'd be happy to help with integration for Rhesus Macaque. By 'new version', are you referring to incorporating Drop-seq tools 2.0? I was just starting to wonder about how...

Exciting! Really just the ability to generate a count matrices for reads falling in introns in addition to reads falling in the coding sequence.

Awesome, I just got a new load of data and so I'll run it with the new version! I'll let you know how it goes.

Is there documentation anywhere on how to setup the binaries to run the new version? When I try to run it with the environment that was working for the previous...

Nope, I wasn't. Sorry I missed that! Will give it a try.

Thanks for the response! I see, that is all useful context. I can certainly try umi_tools with the --method umis flag to see if that helps. But actually I'm just...

OK, thanks for the feedback! I won't worry too much about those cells then for the time being. I suppose I was just surprised by the cumulative fraction only being...

Sorry for the slow reply! Could you provide the complete trace? That likely suggests there is an issue with the clustering in the consensus step?

Hi, thank you for this comment and for using cNMF. It is strange that I'm not getting this error in settings outside of the tutorial and indeed I'm having a...