Colin Davenport

OK, great. What about these (have never tried, but curious about them) ? ``` -m, --mod_base=BASE Modified base of interest, one of: 5mC, 5hmC, 5fC, 5caC, 5hmU, 5fU, 5caU, 6mA,...

Isn't this similar in scope to https://github.com/samtools/samtools/pull/423 ?

@ghuls Wouldn't you want to spare yourself a world of pain and just remap all data to exactly the same reference ? It's a fundamental weakness in the approach -...

I'm not sure this is possible without breaking downstream tools, see https://github.com/arq5x/bedtools2/issues/406

Done, thanks

Nice. I had just started this, but these are the most common issues I see: - truseq and nextera confusion - incorrect delimiters (they make this in excel and inexplicably...

Nope, since they say it doesn't allow custom primers, which we use a lot of. eg for amplicons, Nextera, NEB etc.

Cufflinks is way, way out of date. Why not avoid this and use stringtie instead ?

@jashapiro I would be interested in any approach for dealing with variable bases or "diversity inserts" in modern (2023) BD Rhapsody data. The library structure is detailed here as well:...

You could use a tool like hyperfine https://github.com/sharkdp/hyperfine to measure the speedup when increasing the amount of threads. I suspect it might be overkill to give the tool more than...