Arthur Rand

Hello @Chuang1118, I think the problems you're seeing here are due to the duplicated bedMethyl records. Modkit shouldn't crash the way it is now, it should handle this case more...

Hello @Chuang1118, > Current version modkit (v0.5.0) can handle this issue ? It cannot. If there are two records reporting on the same genomic position and strand for a modification...

Hello @Chuang1118, In case you run into errors such as ``` > Error! Input bedGraph not sorted by chromosome. Sort with sort -k1,1 -k2,2n. ``` I've pushed some updates to...

Hello @WeiHea, Thanks for the question. I'll get your code running and see about the differences.

Hello @tramelliwe, That's a bug. Thanks for bringing it to my attention.

Hello @liscruk, Sorry about the delay in getting back to you. Could you show me the `modkit pileup` command that you used to generate the bedmethyl files? Is is possible...

Hello @liscruk, These are the best kinds of bugs.. happens only occasionally and you have to wait in order to observe the symptom :). My next guess is that the...

Hello @Hedi65, sorry about the delay. > However, the demux function will drop those modified bases. I used the Rapid Barcoding Kit for my sequencing, and de-multiplexing is quite important...

Hello @Chuang1118, Thanks for the question, and sorry for being slow to reply. Normally (i.e. with DNA sequencing) I would recommend using the reads themselves in IGV (or any browser)...

Hello @Aarhus-kga, I tried to reproduce the result using the colo829 open dataset from [epi2me](https://labs.epi2me.io/colo-2024.03/). Here are the steps: 1. Fetch just the region we care about. Currently, Modkit doesn't...