Arthur Rand

Hello @gsukrit, Sorry I forgot to mention this above. There is a [setting in Dorado](https://software-docs.nanoporetech.com/dorado/latest/basecaller/mods/?h=thresho#modified-bases-threshold) where if the probability of a base being **unmodified** is $\ge$ this number the probability...

Hello @rania-o, Could you tell me which version of Modkit you're using with Dorado v1.0.0?

Hello @rania-o, Yes, the modified base models in Dorado v1.0 require you to use either `--modified-bases-threshold 0.0` whilst basecalling/modification calling or Modkit v0.5.0. The reason is that the false-positive rate...

@mnsmar @rania-o thanks for the info let me take a look.

Sorry for the delay @mnsmar and @rania-o, I've found the bug/problem. You have two options. You can use the released Modkit with the following additional `--assign-code` arguments as in this...

Hello @rania-o, Could you tell me which basecalling/modification models you used? If you have not filtered the base modification calls (used `--no-filtering` with `modkit pileup`) I would not be surprised...

Hello @OceaneMion, I apologize about the delay in getting back to you. If you're looking to calculate statistics on the 'valid coverage' at CpG sites. I would use the `--cpg`...

Hello @privefl2, Sorry about the delayed response to your question. The values in the ML tag are stored in 8-bit bins. A value of `0` captures probabilities in the half-open...

Hello @privefl2, Yes you are correct and I think the way you have the summation is better. I'll update this soon. Thanks for noticing this!

@privefl2 I need to do some more in-depth analysis of the implications, but I think summing the probabilities in qual-space then when converting to a probability return the probability in...