Arthur Rand

Hello @ramnageena11, Others have seen this problem when `rustc` isn't updated or installed correctly on your system. Could you try the steps outlined in https://github.com/nanoporetech/modkit/issues/309?

Hello @ramnageena11, Could you try passing a path to the FASTA-formatted _file_ containing the reference sequence? Something like `/home/Documents/genome_assemblies/bc01/ref.fa`, there needs to be an index as well such as `/home/Documents/genome_assemblies/bc01/ref.fa.fai`.

Hello @ramnageena11, You need to create an index for the reference FASTA you aligned the reads to. So if this is the assembly, you should use the same reference sequence.

Hello @ramnageena11, A few things to check. 1. To run `pileup` you need 2 indices one for the aligned, sorted modBAM file (`.bai` usually) and one for the FASTA reference....

Hello @Pombeboy, Could you tell me which basecaller/modification models you used? A couple things you might want to try: 1. In IGV, use the 2-color mode so that the unmodified...

Hey @malton-ont, I think there is a potential sharp edge here. > Bases are "skipped" if the modification probability is below the specified threshold - for a single-mod model like...

Hello @mrvollger, We're working on an article and data release that will demonstrate how we validate the base modification models. Probably the best numbers I can offer are the accuracies...

Hello @mrvollger, > Thanks for the info. Are the filters and distributions built on just the ML tag? Or is there a more complex internal probability estimate within modkit? The...

@Ge0rges thanks for letting me know - I'll get that fixed.

Hello @TKsh6, Sorry about the error. Could you send me a small modBAM that reproduces the problem? It would also help if you could run the command with `--log-filepath` and...