Arthur Rand

Hello @eesiribloom, Just to make sure I'm understanding you correctly. What you're doing is running DMR with `--segment` and with various numbers of test and control cases. Some of the...

Hello @demis001, Sorry for the very delayed response, I've been traveling the last week or so. If you want to use the windowing strategy you've described, you'll need to generate...

Hello @demis001, The argument to `--segment` is a path to the file (to be created) where the segmentation results are written. The rest of the output and options remain the...

Hello @demis001 > I passed --segment my_segment.bed to the above command. If I am not mistaken, this file documented the DMR, and the -o out.bed is the DMC. Please confirm....

Hello @lfpaulin, I'll get a release candidate that allows this ASAP. Sorry that it didn't make it into the latest release.

Hello @lfpaulin, Here's a build that allows .gz references. If you want to build it yourself, I've also pushed the [branch](https://github.com/nanoporetech/modkit/tree/ar/compressed_refs). These changes will make it into the next release...

Hello @aleighbrown, Could you let me know which m6A model you're using (which version)? If you used the automatic model selection, I need the dorado version. Thanks for this analysis,...

Hello @loipf, No there isn't a way to do that with Modkit currently, but I made you a little program called `reads_mods_summary` that does. Here's how you use it: ```bash...

Hello @SuhasSrinivasan, The `--filter-threshold` option is mostly a convienence so that if you have multiple runs or run `modkit sample-probs` as a preliminary step that you don't need to re-run...

Hello @SuhasSrinivasan, Not quite. The routine for automatic threshold calculation collects all of the call probabilities`*`, and determines the value of the 10th percentile. It will not attempt to calculate...