Devon Ryan
Devon Ryan
It's been a number of years, but I recall that that should work. I don't recall needing to exclude anything.
No particular reason, a 1% difference either way has no biological meaning. I guess a proper rounding would be a bit nicer though. I'll leave this open as a reminder...
0.1 is fairly reasonable. Please note that you end up filtering out any sequence artifacts and stuff like that, which will randomly appear with longer reads.
It's the count on the non-C strand, since it's easier to assess whether there's a variant using it.
In theory I suppose it wouldn't be immensely difficult. PRs welcome :)
There isn't, maybe bismark has an option for that? I guess I could add a GpC context output otherwise, though I'd need to look at some NOMe-seq data to see...
OK, if you end up really not finding anything else then just (privately) send me a small bit of a BAM file showing a few decently covered positions. We can...
@rgilsbach it was never popular enough for me to implement. I need to push out a new release of MethylDackel, so maybe possibly I can incorporate this into that...but I...
At the moment I'm not sure that's possible (for what it's worth, PBAT was just coming out when this package was created). Can you point to any convenient (ideally smallish,...