Winston Timp

This is helpful thanks. So basically you have also disabled the ctrl-P and ctrl-F. I did something similar but also remapped documentsearch:start to ctrl-S. However, it doesn't address the core...

Firefox (and most browsers) seem to aggressively capture ctrl-N for example. Surprisingly, you can get around this with chrome by making the webpage into an app, but it doesn't solve...

100% agree. I use notebooks for data exploration rather than actual development per se. This is why I don't want to break my emacs muscle memory to use notebooks.

So - we looked at this somewhat in our paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7704922/) and didn't see that it really changed the correlation. Are you filtering out GpCpG sites?

Ok - I have added readgroup ID and SM information by adding an -R tag to my bwa command, but now I get a different error: "IndexError: list index out...

They are single end reads. I put (perhaps naively) the fully aligned bam into the -B, and the split reads (extracted with "extractSplitReads_BwaMem" from lumpy) into -S What I'm trying...

I actually plan to just be simpler than that for now - and use bedtools just to estimate coverage in the region - I'm using amplicons so I know where...

Or conda for that matter?