Laura White

I second this feature request. One specific use case would be taking basecalled nanopore sequencing data where modification information is stored in MM and ML tags of an unaligned BAM...

Re-bumping this in hope of a response.

Thanks for all the work developing this. Would be great if this description of the column outputs were added to the documentation for bedgraph pileup [here](https://nanoporetech.github.io/modkit/advanced_usage.html#pileup).

Looks like we have a whole bunch of `record XXX has improper data, MN tag length X and seq length Y don't match`. These are tRNA sequencing data so those...

The log was a little too big to attach so I've split it in two parts. [mkextract_postremora_part1.txt](https://github.com/user-attachments/files/16041882/mkextract_postremora_part1.txt) [mkextract_postremora_part2.txt](https://github.com/user-attachments/files/16041883/mkextract_postremora_part2.txt)

That reduces the % of reads failing, and the ones that fail now say `record has improper data, malformed MM delta list`. I couldn't find MN in the sam spec,...

Thanks @ArtRand for the quick feedback. I read through that section of the spec and then through various ModKit documentation and GH issues over the past week but it's a...

Art, just to clarify, how does this column interact with thresholding in `modkit pileup`? If I pass a filter of 0.98, does every read aligning to a given location with...

Hm. Even after reading your explanation and playing around a little I'm not 100% sure what the functionality of the "on the map" tick box is intended to be, so...

Hi all, I am also trying to troubleshoot this issue with Sam, and it's a bit unclear what files should be generated during this step. `bonito basecaller dna_r9.4.1 --save-ctc --reference...