Arthur Rand

Hello @Ge0rges, I tend to agree. I find myself relying on the "command" comments in VCF files and PG records in BAMs all the time. There is a lot going...

Hello @liliaevgeniou, The `mod_qual` values (which I will be renaming to `mod_probability` in the next minor version bump) are derived from the ML tags as you guessed. However, since the...

Hello @MaestSi, Sorry for the delay and thanks for the question. Probably the easiest thing is to convert the bedMethyl into a bedGraph or bigWig file. You would have to...

Hello @Raya-Faigenbaum-Romm, I strongly recommend using `dorado aligner` ([docs](https://github.com/nanoporetech/dorado/?tab=readme-ov-file#alignment)) for mapping an BAM with base modification information (modBAM), you can pass the `-Y` flag if you want to capture non-primary...

Hello @JoukjeKloosterman, In the latest release `modkit` still requires the strand information in the `--include-bed` files. I wanted to remove this requirement in 0.2.4, but it didn't make it. If...

This feature has been implemented.

Hello @JoukjeKloosterman, The problem is that the Fasta parser currently in modkit (and in 0.2.0) will silently drop gzipped records. One item on the roadmap for the next release is...

Hello @marceelrf The data used in this tutorial is a little old, and as a result the base modification tags in the BAM don't have the MM-flag and implicitly denote...

Hello @mattloose, > In some circumstances this can lead to different methylation calls for the same read in a dataset. I would expect that when the pass threshold varies slightly...

> The problem I have with all of this is that a single position in a single read can be called as methylated or not methylated dependent on the rest...