Arthur Rand

Hello @zhihao6201, Sorry about this, there is a bug where if Modkit cannot get enough GPU memory it can stall. I'm working on a fix. In the mean time there...

Hello @billytcl, This column will be included when more than one motif is used. So for example if you added `--cpg --motif CGCG 0` you will get this column indicating...

@jkh00 could you tell me the output of `modkit --version`?

Hello @sxlaas, This is a bit more of a Dorado question, but I think we can address it here. There was a change in the 5mC_5hmC model from Dorado version...

@sandraionescu Ah ha! Thanks for catching that!

Hello @SimonChen1997, You cannot filter the bedMethyl as you have done prior to using `modkit dmr`. You need to have the records for each base modification (4mC and 5mC in...

Hello @SimonChen1997, Sorry for taking so long to respond to this thread. The short answer is the `C` means "any cytosine modification". The reason this shows up is at position...

Hello @KunFang93, Could you tell me which version of Modkit and Dorado you've basecalled/modcalled your data with? If you're using Dorado v1.0.0 you _must_ use Modkit v0.5.0. To your questions....

Hello @KunFang93, > However, when I check the 200nM free Hia5 sample, the 10th percentile value is only around 0.55–0.56, which still seems quite low. I would have expected a...

Hello @KunFang93, I've attached a build that allows "per-position" filtering. You can also build it from [this branch](https://github.com/nanoporetech/modkit/tree/ar/per-pos-filtering). To use it, add the `--position-thresholds` flag to your `modkit pileup` command....