Arthur Rand

Hello @Fu-Yilei, I apologize for the delayed response. When you use the `--include-bed` option `modkit extract` will only output mapped modified base positions. I believe there is a log line...

Hello @Fu-Yilei, Using `localize` is an interesting idea. The prototype that I have uses the bedMethyl and is a pretty simple "bedtools-like" operation of aggregating methylation frequencies around genomic features....

Hello @Seongmin-Jang-1165, The `ref_position` is always the position as it would be in the FASTA reference. So a smaller `ref_position` is always toward the 5-prime end of the transcript since...

@Seongmin-Jang-1165, You should be able to use a modBAM directly in IGV. Which version do you have? I'm using 2.19.1. To get the coloring, you need to specify color by...

Hello @Seongmin-Jang-1165, I generally recommend making the bigWig file at the same time as performing pileup, there is an example in the [documentation](https://nanoporetech.github.io/modkit/intro_bedmethyl_merge.html#convert-bedmethyl-to-bigwig). ```bash # you can run pileup and...

Hello @Seongmin-Jang-1165, I think the problem is that you're switching references. If you aligned to a transcriptome (looks like you did?), you need to use that reference throughout the analysis....

@Seongmin-Jang-1165 Sorry I think I missed this detail in your first comment: > the one thing is that I generated the bedmethyl file with older version, so the transcript/gene decription(gene...

Hello @KunFang93, That's a good idea, both of those commands are due for a little refresh. One caution about splitting the bam, depending on how you're doing it, you can...

Reopening this to track the work.

Hello @eesiribloom, Looks like the [.beta](https://github.com/nloyfer/wgbs_tools/blob/master/docs/beta_format.md) files could be converted into a bedMethyl table if you can join on the chromosome and positive position of the CpG. That being said,...