Devon Ryan

Can you suggest any public dataset or other data source I can use for debugging this?

Is this method published anywhere? I'd be interested in reading exactly how all of the library prep is working. The `ModA` and `ModB` case should be easy to implement, but...

Interesting. Feel free to email me directly so I can keep everything confidential.

I think we need to first distinguish what you mean by the first 10 bases of a read. Are these the first 10 bases produced by the sequencer (what I...

Correct, since it's impossible for the tool to know what the original length was. However you do know what it was, so you can just subtract 10 from that.

The adapter is on the other end of the read. You don't need to know how many bases were quality trimmed, if the bias is in the first 10 bases...

Is there a reason you're quality trimming the beginning of your reads? That's extremely unusual. Adapters and lower quality are at the other ends of them.

Make sure those are regular commas and not getting converted to some weird comma-like unicode characters. That's my only guess as to what's going wrong there. Otherwise that error message...

There can be up to 4 reverse reads in BS-seq, and `--nOT 10,0,10,0` will trim off the first 10 bases of those arising from the original top strand regardless of...

I'll definitely look into the parsing bug, thanks for reporting it :)