Arthur Rand

@OceaneMion > have another question, what kind of statistical test will you use to see if methylation at CpG sites is random or not, do you think Kolmogorov-Smirnov is appropriated...

Hello @selmapichot, Sorry I missed this question. All CpGs that have modified base information (including canonical calls) will be included in the bedMethyl as long as they pass the [pass...

Hello @setshabaTaukobong, Did you run alignment concurrently with basecalling? To run `modkit pileup` you need to have reads aligned to a reference. You can inspect the base modifications on a...

Hello @setshabaTaukobong, You can perform alignment during basecalling by providing a reference, or if you've already basecalled the reads I would align them to the reference using `dorado aligner`. I...

@setshabaTaukobong any luck?

Hello @uuwuyi, > However, in the "modified base code and motif" column of the modbed file, I'm not sure exactly which file you're referring to. Could you tell me the...

Hello @uuwuyi, The fourth column of the bedMethyl table should only have the modified base code, the snippet you have here is what I would expect. Version v0.3.0 had a...

Hello @uuwuyi, Thanks for sending the logs over. It looks like the overall level of modification in this sample is low. From the logs you can trace the progression of...

Hello @uuwuyi, Did you use `--min-sites 30` and `--min-frac-mod 0.5`? Could you attach the log?

Hello @ShokodkoMariia, This is a pretty common request, so I'll try and get it into an upcoming release. In the mean time, you can convert the bedMethyl file into a...