Arthur Rand
Arthur Rand
Hello @kamaloxfordpathology, The `modkit localize` command is intended for this task, however it is probably not quite as fully-featured as the command in `deeptools`. Depending on what you're trying to...
Hello @Tang-pro, The modified base information is contained in MM/ML auxiliary information tags, usually in SAM format. There is a specification [here, see page 7](https://samtools.github.io/hts-specs/SAMtags.pdf). Although it is possible to...
Hello @Tang-pro, That's an interesting question! For most of the functions in `modkit` you'll want to use the "unified reference genome". For example the [differential methylation](https://nanoporetech.github.io/modkit/intro_dmr.html) commands all require a...
Hello @Tang-pro, > The pass.fq.gz file provided by the sequencing company already contains methylation modification information and polyA tail length. It's hard for me to recommend a method to use...
Hello @hannan666666, We recommend testing base modification models on synthetic strands. We've recently published a [blog post](https://labs.epi2me.io/mod-validation-data/) describing how we derive the model performance metrics. Unfortunately, the 4mC validation data...
Hello @Tang-pro, You should use the FASTA that you aligned the reads to. However, this argument is only required if you're using the `--motif` options.
Hello @ralanany. The Modkit command you've found is correct for performing differential methylation on multiple samples. You can use the `score` column or if you want to perform [single-site](https://nanoporetech.github.io/modkit/intro_dmr.html#3-detecting-differential-modification-at-single-base-positions) analysis...
Hello @zaka-edd, I'm right in the middle of some requested updates to `modkit extract calls`, one thing is adding BAM Aux tag information. I don't know if it will make...
Hello @cmdcolin, Sorry for the terribly long response time (new Modkit features are coming!). You could filter the bedMethyl to only positions that match the reference and/or remove records with...
Hello @Ge0rges, That's no good, thanks for the heads up. Working on fixing the last few (known) bugs before a release, so I'll add this one to it.