Arthur Rand

@baibhav-bioinfo > if i want to analyse the sites which are only present in one of the conditions Do you mean looking for intra-condition variability? I.e. differentially methylated regions between...

Hello @baibhav-bioinfo, Another user [discovered a bug](https://github.com/nanoporetech/modkit/issues/358) where when some samples don't have alignments to a contig it will cause the whole contig to fail. I have posted a build...

Hello @baibhav-bioinfo, I'm working on some improvements to the DMR module right now. I like the intuition behind adding a pseudocount, but I don't know how it would impact the...

@baibhav-bioinfo working on it.

Hello @DelphIONe, The `valid_coverage` is the number of base moficiation calls (modified of any class or unmodified) that pass the filter threshold probability. For more details, the [documentation](https://nanoporetech.github.io/modkit/filtering.html) has some...

Hello @DelphIONe, > If I have 0% modification for one position with 100 reads, and I mix them with another 100 reads with 50% modification for the same position, shouldn't...

Hey @mrvollger, Thanks for the test data! I'll get to this once I get a POC of the new thresholding technique* out. * Idea is to make a threshold per...

Hello @hannan666666, These entries are likely due to a few reads with A>C mismatches aligned to AVV motifs which will have m5C calls on the Cs. If you're interested in...

Hello @jmlavigne1, > I'm unsure who to reach out to about this, You've come to the right place! > 1. Why can't I use a bam file that has been...

Hello @jmlavigne1, There are two problems with the command you have: 1. The input needs to be a bedmethyl table, not a modBAM file. 2. The `--regions` argument should be...