Arthur Rand

Hello @GregorD96, You're correct, there isn't a way to get this information from `pileup` right now. I'm working on adding some additional data to the `pileup` output and considering a...

Hello @psidhwani, > I have the same question. Could the output of sample-probs help with this in some way? For example, if we have the percentile ranks of each of...

@Ge0rges yes that's correct. In 0.2.3 (out this week) `dmr multi` will work at the individual base level.

Hello @Ge0rges, Are you trying to perform single-site analysis with multiple samples? My previous comment ended up being incorrect. There are two things you can do: 1. Test two conditions...

@Ge0rges, You'll need to script up the loop then. There is no reason that `dmr multi` couldn't do the loop for you. The implementation in `multi` isn't my favorite so...

Hello @Ge0rges, I've added the ability to use multiple mod-BAMs as input to the `modkit entropy` alpha feature (see the above thread for a build). I took a quick look...

Hello @mocherry, You can use the `--motif DRACH 2` argument to `modkit pileup`, the [documentation](https://nanoporetech.github.io/modkit/intro_bedmethyl.html#narrowing-output-to-specific-motifs) describes how to do this. You'll need a reference sequence, but it will find the...

Hello @IanCodes, I would use columns 1, 2, 3, and 4. Described below: | column | name | description | type | |--------|-----------------------|--------------------------------------------|-------| | 1 | chrom | name of...

Hello @IanCodes, You can certainly combine them. The bedGraph format doesn't have a nice way to represent different modifications, however, so you might want to combine them separately. ```bash cat...

Hello @lkwhite, To be honest, I'm planning on deprecating the `--bedgraph` flag since you can [generate the bedGraph](https://github.com/nanoporetech/modkit/issues/210#issuecomment-2181706374) from the bedMethyl, but having an un-documented output format is poor form...