Arthur Rand

Hello @eesiribloom, A couple things to quickly check. 1. Run `modkit modbam check-tags [-n 10000]` on both samples to make sure the MM/ML tags made it across OK. Sometimes using...

Hello @eesiribloom, > Would this change the proportions so drastically to go from CpG only to global 5mC? Yes I think it would. In your first sample you're looking (summarizing)...

Hello @Flower9618, You'll have to use `modkit extract calls` ([documentation](https://nanoporetech.github.io/modkit/intro_extract.html#tabulating-base-modification-calls-for-each-read-position-with-extract-calls)) to determine the co-occurance of base modifications on a individual read level.

Hello @Flower9618, The easiest way is to minimize the number of conversions. I recommend staying in (mod)BAM as much as possible. `dorado` will perform adapter trimming and mapping (find the...

Hello @Flower9618, Yes they should be. I'm going to add a "check" command to a future version of Modkit that will help to make sure the tags are correct. But...

Hello @rowanhowellGE, You can't right now, but I can see about adding this as a feature.

Hello @ethan-mcq, Something like that is possible. For a CpG to be "covered" would you mean that the CpG has at least 1 passing base modification call? This feature feels...

Hello @ethan-mcq, I see. Perhaps a very lightweight version of `pileup` that can be run quickly would help. I can look into performing this tabulation during `extract`, I'd just want...

Hello @lucagu1965. That shouldn't happen, could you share the input file with me? If you send me an email at art.rand [at] nanoporetech.com, we can work out how to share...

Hello @lucagu1965, Sorry for the delay, but I think I've tracked down the problem and made a fix. Could you try the build attached here? Thanks.