Arthur Rand

Hello @billytcl, > I'm guessing it shouldn't be as bad as the threshold being ~1, but for consistency I should probably call even the v0.9 dorado runs with include-bed as...

@jcolicchio-soundag, I don't know how or why increasing the size of the `--include-bed` file should make a difference. None of this code has changed recently, but could you tell me...

Hello @billytcl, Sorry about that. I'm working on making this faster and less resource hungry. Could you try passing `--ignore-index` or `--queue-size 1000`? The former will almost certainly use less...

Hello @billytcl, I'd recommend using `--ignore-index` to unblock your workflow in the short term. The whole `pileup` and `extract` apparatus is going through a re-write at the moment and the...

Hello @billytcl, Sorry for the delay. I did a quick test on some ~30X C+A all context data and `--ignore-index` didn't change the run time at all. It's still not...

Hello @reJELIN, These codes are the ChEBI code for the base modification. In your case 17802 is [pseudouridine](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17802). Only a few of the base modifications have single letter codes (you...

Hello @Tang-pro, Sorry for the terribly long response time (new Modkit features are coming!). I don't have a specific recommendation regarding the effect size other than making a classical "effect...

Hello @WeiHea and @shuiliunian this issue looks pretty similar to https://github.com/nanoporetech/modkit/issues/438, could we consolidate them? I can work on getting a comparison together.

Hello @WeiHea, In Nanopore data often times the base_qual is correlated with modification probability. So filtering on base_qual could bias your modification estimates. Do you find this to be the...

Hello @Chuang1118, Sorry about the crash. Could you run the commend with `--log $log_filename` and attach it here?