Arthur Rand

Hello @kamaloxfordpathology, There isn't a function like that in Modkit, but I've asked my team if there is a recommended tool. I'll circle back.

Hello @Proy321 sorry about the delay. > Does this indicate that the proportion of h (5hmC) is lower compared to m (5mC), and therefore this site should be interpreted as...

Hello @Proy321 sorry about the delay. The interpretation of the reads will always depend (at least a little) on the biological system you're studying. The sequencer and the analysis software...

Hello @privefl2, Sorry for the delay getting back to you. There is a description of the columns in `modkit extract calls` [in the documentation](https://software-docs.nanoporetech.com/modkit/intro_extract.html#tabulating-base-modification-calls-for-each-read-position-with-extract-calls). It's hard for me to know...

Hello @kamaloxfordpathology, Could you run `modkit summary $bam` with the automatic threshold detection and the `--only-mapped` flag and let me know what you get? You may also want to try...

Hello @kamaloxfordpathology, thanks let me circulate this with my team. Could you run the same command with `--mod-threshold m:0.9` at your convenience? Also could you tell me if you're using...

Hello @yyzhou4535, Very sorry about the delay getting back to you - a big Modkit pileup update is coming! I need a little more information about your biological question to...

Hello @gpsolorio I don't have a recommendation right now, but this is something I'm actively looking into. I'll let you know.

Hello @gpsolorio Not yet. Still trying to clear my desk of some other work.

Hello @assafgrw, I apologize, this example in the documentation is out of date. I'll update it with the next version release. You need to specify how to calculate the methylation...