Arthur Rand

Hello @bebert30, The latest version of modkit ([v0.2.5](https://github.com/nanoporetech/modkit/releases/tag/v0.2.5)) should be considerably faster to calculate DMR scores and pvalues ([details](https://nanoporetech.github.io/modkit/dmr_scoring_details.html)) at single bases. Please give it a try at your convenience.

Hello @bebert30, It looks like you used a 5hmC/5mC model, so the output of `modkit dmr` will consider both of these modifications. The [score](https://nanoporetech.github.io/modkit/dmr_scoring_details.html#likelihood-ratio-scoring-details) takes multiple modifications into account, so...

Hello @martabaragli, Are the input mod-BAM files aligned and sorted (with an appropriate index available)? The parallelism in `modkit extract` is over genomic intervals, so if you have an _unaligned_...

@ericmsmall There is no correction applied, the MAP-based p-values are all calculated independently and in isolation.

Hello @billytcl, Making the output of `pileup` directly consumable by `dmr` is already on the roadmap actually. You _can_ compress the bedMethyl output on the fly: ```bash # passing `-`...

Hello @ppapasaikas, I'm a little confused how you're generating `pileup_B.bed`. All of the most recent versions will not let you pass the `--filter-percentile` (`-p`) option along with the `--no-filtering` flag....

Hello @ppapasaikas, You may get different results from running `modkit pileup` with specified thresholds compared to first running `modkit call-mods` with specified thresholds _then_ using pileup because the filter thresholds...

Hello @ppapasaikas, If you can share a BAM that exposes the issue that would help a lot and I'd be more than happy to take a look. Thanks!

@ppapasaikas Any update, keen to investigate the problem if you're willing to share a BAM that exposes it.

Hello @lance0499, Currently there isn't a way to perform a region-based pairwise comparison using multiple replicates where the replicates are combined in some way. I'm working on something, but it's...