Arthur Rand

Hello @jmlavigne1 The `--chart` option requires a path to write the HTML file to so you need: ```bash modkit localize \ --chart localise_chart_file.html \ #

Hello @jmlavigne1, > I think that I incorrectly assumed that the "0" on the x-axis was the center of the gene, and that the gene was flanked by a range...

Hello @jmlavigne1 > 1.) so if my region.bed is 4 19031768 19033832 are you saying that the "0" on the x-axis will be the midpoint between 19031768 19033832? Correct. Regarding...

Hello @partha434, The `pileup-hemi` command is meant for duplex Nanopore data where you have base modification calls on the (+)-strand and the (-)-strand combined into a single duplex read. Then...

Hello @pkerbs, A couple things. > For that I tried using modkit summary on a sample where I don't expect any reads carrying methylation at any position: All of the...

Hello @pkerbs, No problem at all. More than happy to help. This command: ```bash modkit extract calls \ --filter-threshold 0.85 \ --mod-thresholds m:0.85 \ --threads 16 \ --mapped-only \ --ignore-index...

Hello @pkerbs, > So I filtered now like this awk '$14=="m" && $20=="false" {print $1}' | sort | uniq | wc -l which should give me the number of reads...

Hello @Taylorain, > 1. Could the [email protected]_inosine_m6A@v1 model still be immature or require further validation? We have recently published a [blog post](https://epi2me.nanoporetech.com/rna-mod-validation-data/) with synthetic ground-truth strands that you can download...

Hello @lubitelpospat, I'd be more than happy to review a PR. FWIW I'd like to add more "query" commands and maybe a small python library to help parse the DMR...

Hello @lubitelpospat, This is similar to the [another question](https://github.com/nanoporetech/modkit/issues/469). tl;dr: For a given position `modkit pileup` reports all base modifications (including unmodified) where there is at least one valid read,...