Arthur Rand

@ArnavBharti @PRIYANKA-22091995, Any update on this?

@ArnavBharti @PRIYANKA-22091995, Any chance you could update guppy to at least `6.3.2`? I downloaded v3.5.1 and don't see the options you'll need. If you're using R9 data, you could probably...

Hello @VasLem, When using `modkit pileup --cpg` all CpGs with at least 1 read of valid coverage will be emitted in the output. If you want all CpGs with _any_...

Hello @OceaneMion, If you're using the same assembly (i.e. reference), you could use `modkit dmr pair` you'll find the [documentation](https://nanoporetech.github.io/modkit/intro_dmr.html) online. This command will find the sites that have differing...

@OceaneMion Maybe I'm not understanding what you're trying to do. Are you trying to determine if there are differences in the levels of methylation between two _different_ contigs? For that...

Hello @OceaneMion, I think what you want is to use `modkit pileup`, find the [documentation](https://nanoporetech.github.io/modkit/intro_bedmethyl.html) online. If you need to measure the correspondence between two reference positions this table is...

Hello @OceaneMion, During pileup, each read's base modification probability (`mod_qual`) is converted into a base modification _call_, i.e. a decision as to the state of the base as modified or...

Hello @OceaneMion, Basically, yes. If you have a model that predicts more than one modification at a base (e.g. 5hmC/5mC at cytosine bases), you'll have a categorical distribution where the...

Hello @soniacruciani, Currently to get the information you want you'll need to use `modkit extract calls` then group by the reference position and modification code and aggregate. Something like this:...

Hello @soniacruciani, That is an interesting idea, I'll give it some thought. Do you have some examples of these two cases? My intuition would be that the modified base model...