Arthur Rand

@Flamefire Thanks for noticing that, this is pretty easy to fix. If I push something to `master` would that help or do you need a full release?

Hello @umranyaman, It sounds like you want a bedMethyl with all of the counts aggregated, as through you had run `pileup` without partitioning on the HP tag. I would use...

Hello @umranyaman, Regarding using the ungrouped reads, it depends on what you're trying to do. The ungrouped reads are ones that don't have the haplotag, so I imagine this means...

Hello @umranyaman and @vaishnavpvarma As of Modkit v0.6.0 there is much more robust CRAM support and a `--phased` option for exactly the use case you have here. Now instead of...

Ok, I'll take a look into it.

Hello @Proy321, > Start: 813563 | End: 813564 – Since the counts show h:1, m:2, does this indicate that one strand of DNA carries 5hmC and the other strand carries...

Hello @Proy321 I apologize for the delay. > When both h:1 and m:2 are present at a given position, does this indicate that 5mC is being converted into 5hmC? I...

Hello @Proy321, > Specifically, I am trying to understand how both modifications can be present at a single position rather than being assigned to distinct positions. For example, I observe...

Hello @brambloemen, Could you try `--interval-size 50000` and `--chunk-size 12` (assuming you have also set `--threads 24`). You may also set `--queue-size 500` or less (with or without the above...

Hello @jmlavigne1, What I've done is use the bedGraph files directly, or parse them into python and make my own plots depending on the experiment. Are you thinking maybe something...