Arthur Rand

Hello @Macdot3, You can skip filtering on `read_position_max` so the code from [#87](https://github.com/nanoporetech/modkit/issues/87) becomes ```python import polars as pl X_calls = pl.read_csv("modkit_calls.tsv", separator="\t") X_aligned = X_calls.filter(pl.col("within_alignment") & ~pl.col("fail"))\ .with_columns([ (pl.col("forward_read_position")...

@Macdot3 any luck here?

Hello @Macdot3, I'm a little unclear about what you're trying to do, exactly. Are you trying to determine the genome positions with base modifications in the mitochondrial genome? Are you...

@Macdot3 I really think what you want is the output from `modkit pileup`. > I want to calculate the percentage of methylation at each modified base called on each sequenced...

Hello @Macdot3, I'm pretty sure you want the `fraction modified` value, [column 11](https://nanoporetech.github.io/modkit/intro_bedmethyl.html#bedmethyl-column-descriptions). The value for `N_valid` can differ from samtools depth for a couple reasons: 1. A read's modification...

Hello @davidsilvapires, There isn't a command exactly like that. Although I've gotten a similar request before - so maybe it's time to add one.

Hello @davidsilvapires, A feature like this called `modkit stats` is available in [v0.4.1](https://github.com/nanoporetech/modkit/releases/tag/v0.4.1) (actually it was released in v0.4.0). Don't hesitate to open a separate issue if you have any...

Hello @mocherry, You can use it directly, but it may not be very helpful - to be honest. The [bedGraph](https://genome.ucsc.edu/goldenPath/help/bedgraph.html) format is more suitable to visualization. You can use the...

Hello @mocherry, Sorry for not explaining. `bash` is just a commonly used [shell language](https://en.wikipedia.org/wiki/Bash_(Unix_shell)). If you don't have an environment like this, that's not a problem. You can run `modkit...

Hello @bebert30, Yes I would split the reference into chromosomes. Although this will only help the memory usage - not the processing time. What you can do to decrease processing...