diego-rt

Sure! Here it goes:  And one last thing: we are really interested in using HMMRATAC with our ATAC-seq data but unfortunately it doesn't seem to work with CSI indexes,...

Apologies for the delayed reply! Oh that's great to hear about HMMRATAC! Do you have an estimated release timeframe in mind? Yes, the chromosome names are different becase some are...

Hello, I was wondering whether you have any updates, workarounds or suggestions on how to address this? @taoliu @EvanTarbell Just for clarify, the problem is that when working with chromosome...

Hey guys, just want to note in this thread as well that .clone() does not work on maps that carry a groupKey. This works: ``` #!/usr/bin/env nextflow nextflow.enable.dsl = 1...

Actually yes, the `+` syntax seems to work just fine. It doesn't seem to preserve the groupKey of the object though. Btw, also another thing that seems to be missing...

Hey there, Thanks a lot for the potential solutions! I commented it out and will see if it makes any difference but will likely take a few days to get...

Hi @cjain7 Does this mean that it's not possible to map to genomes larger than 4G while getting accurate mapQs? For minimap2 this would be the case in the absence...

Ah fantastic! I had found the corresponding line in your code and was about to edit it, but this is much more convenient. I would say it is not rare...

I can confirm that `--buffer-size=16000000` does the job

Just want to add that I completely agree that it would be fantastic if cutadapt could incorporate ONT-centric options. Currently there is no tool that adequately deals with that. In...