Arthur Rand

Hello @Rpowellnz, You certainly need to remove any of those HTML tags at the start. The BED file should be a plain text file with 3 or 4 tab-separated fields:...

@Rpowellnz The [latest version](https://github.com/nanoporetech/modkit/releases/tag/v0.3.2) will report out which file is failing to parse. Could you confirm that it's an issue with the argument to `-r` (the regions file)?

Hello @colindaven, How are you producing the basecalls/base modification calls now? Are you using dorado/remora? Your commands look fine to me. One note is that `modkit` will not emit a...

Hello @colindaven, Sorry for the delay. Just to recap, if a genomic position has 0 valid coverage, it won't be written in the bedMethyl/bedGraph table. The `--no-filtering` flag essentially disables...

@colindaven Any luck here?

Hello @hassebossenbroek, Is it possible that there are some memory guards in your HPC environment that aren't visible to `modkit`? Can you increase the memory limit in [apptainer](https://apptainer.org/docs/user/main/cgroups.html#memory-limits)? 62Gb of...

@hassebossenbroek any luck?

Hello @hassebossenbroek, If you have very non-specific methylation the "exhaustive search" step can take quite a long time. The first thing I would try is `--skip-search`, there are other tips...

Hello @Ge0rges, That's a good idea (thanks), especially for mods on different primary bases. Right now you'd have to do it through a pipe. ```bash $ modkit adjust-mods ${bam} stdout...

Hello @angelluigi, Your command looks fine. The algorithm in `pileup` only performs counting, so when you see a results such as 700 of 1500 reads reporting 6mA, that really just...