Arthur Rand

Look like this was taken care of by the Dorado team.

Hello @vzg100, I was able to replicate the problem. It appears that when you run `dorado aligner` with fastq input it does not keep the MM/ML/MN tags. Instead of converting...

Hello @vzg100, Dorado will handle that as well ([barcode docs](https://github.com/nanoporetech/dorado/?tab=readme-ov-file#barcode-classification)). Make sure to use the latest version >=0.5.2, before that there was a bug with trimming the modified base tags.

Hello @vzg100, Maybe I'm missing something obvious, but could you partition your reads based on the `BC` tag? ```text $ samtools view -bh --tag BC: ${bam} -o ${barcode_bam} ``` All...

@vzg100 any luck?

Hello @vzg100, Could you elaborate on what exactly didn't work? Where are you loosing the base modification calls? You should definitely _not_ need to basecall your data twice. At the...

@qiangfu-eu could you tell me which versions of modkit and modbam2bed you're using? Also let me know if you see anything unusual in the modkit log? Also if you could...

@qiangfu-eu one more quick check for me if you would: run the pUC19 BAM with modkit using `--no-filtering`. I want to try an understand the discrepency in valid calls. The...

Hello @qiangfu-eu I've run some tests on my side directly comparing the two programs on larger modBAMs. So far I have not been able to reproduce the difference in valid...

@ArtRand Great. I got the BAM. I'm assuming from the header that the reference sequence you're using is the one from NEB pUC19 ([fasta](https://www.neb.com/-/media/nebus/page-images/tools-and-resources/interactive-tools/dna-sequences-and-maps/text-documents/puc19fsa.txt?rev=6e10f4c4a4234d638e401cd2f4578ef0&hash=87869334CC7AC2B6D7A45D918D74E598)), correct? Linked from [this page](https://www.neb.com/tools-and-resources/interactive-tools/dna-sequences-and-maps-tool).