Devon Ryan

There's not a way to do that at the moment since no one showed me a use-case requiring it. How is it that the insert size is having such an...

Sounds similar to the issues with ATAC-seq. I worked with a student for a while who had WGBS data from a kit like this but I don't think she ran...

Read 2 isn't from the CTOT strand, it's also from the OT strand. Strands in this case refer to the strand that the original fragment came from. You're only sequencing...

I suppose so. Keep in mind, though, that this will end up being per-base (overlapping a CpG) per-read, so the numbers will probably look disturbingly high.

@nchernia I'll see what I can do. The functions that filter reads by MAPQ/flag are buried pretty deep in the code. The phred filtering stuff happens for each base, so...

Good question, just include a link to the repository. I'll mention that in the readme for anyone else wondering. If I ever have a bunch of extra time maybe I'll...

Bioarxiv is the path of minimal effort :) I agree, though, that submitting to bioinformatics as a tool paper wouldn't be too much effort.

An individual position can only contain information on a single strand, since only C-methylation is measured. However if you use `--mergeContext` then the resulting metrics are merged across strands/neighboring bases...

There's no option for that at the moment, since most other BS-seq aligners don't produce that information. I guess I could add it if it's there. What's that tag called...

Regarding `OMP_NUM_THREADS`, that one should probably get skipped since a lot of us have had to force it to 1 to not kill our cluster nodes (this is due to...