Dorado input

[Qvdauwer]

Dear Shian,

Nanopore now suggests using Dorado and Modkit as a replacement for Megalodon for the purpose of methylation calling using nanopore reads.

I like NanoMethViz and would like to use it for this data as well.

would it be possible to make an update that can reads files produced using this method?

Here is an example of the table made in R of the .tsv produced this way: Dorado tsv file.txt

I think this is quite similar to the nanopolish example .tsv structure.

Best regards, Quentin

[Shians]

Thank you for this, I've been working on supporting bam files with mod codes, but this format is also definitely useful to support.

[osvatic]

Has there been any progress on a dorado input for nanomethviz?

Using the bam files with the mod codes would be useful. The modkit pileup output could be a good input file. It produces a bed file, which is smaller than the bams.

[Shians]

@osvatic

At the moment I've implemented support for modbam files, the usage is described here: https://bioconductor.org/packages/release/bioc/vignettes/NanoMethViz/inst/doc/UsersGuide.html#using-bam-files-with-modification-tags

the modbam_to_tabix() function allows this data to be converted into the standard tabular form used in NanoMethViz. I feel like this sufficient functionality for dorado output but if people tend to throw away the modbams and only keep the tabulated tsv/bed then I can work on supporting that as well.