Arthur Rand

Hello @KevDonn, Your command looks fine, however something to consider is that `modkit extract` is intended for _read-level_ interrogation, so you get one row per position per read. As a...

Hello @OceaneMion, It depends on your biological question. Of course you can calculate the ratio however you want, a couple ways I can think of: 1. Number of modified CpG...

Hello @mvolar, Using a Beta distribution to model the probability of modification at each position is a reasonable way to do it, in fact, this is how the [MAP-based P-value](https://nanoporetech.github.io/modkit/dmr_scoring_details.html#map-based-p-value)...

Hello @mvolar, Since you have two conditions, one thing you might want to try is using the [segmentation function](https://nanoporetech.github.io/modkit/intro_dmr.html#segmenting-on-differential-methylation) in `modkit dmr pair`. From there you can get regions of...

Hello @mvolar, One thing you could try is increasing the `--significance-factor` in `modkit dmr pair --segment`. Increasing this number will have the effect that smaller differences (or less evidence) will...

@OceaneMion I believe I've answered this question in https://github.com/nanoporetech/modkit/issues/192?

Hello @faulk-lab, That's not likely a feature we're going to add I'm afraid. Especially considering that 3-letter alignment (with tools like Bismark) is something we're trying to avoid. May I...

Hey @faulk-lab, An entropy calculation certainly something I can add. Entropy is especially interesting when you consider that Nanopore reads will have 5hmC as well as 5mC. I'm also actively...

Sounds good, I'll hand over a build when it's ready, thanks!

Hello @faulk-lab, I have a branch with an entropy calculation to try. A quick disclaimer, I would consider this a "alpha"-level feature and certainly not production-ready. There is some missing...