read-region-frequency - not working? :o

[icetea-s]

Hello!

I am working with cfDNA, and am using nanopore sequencing. Hence, this seems like the tool for me.

However, I am trying to run the mbtools read-region-frequency -r ATLAS.tsv -g REF.fna --cpg SAMPLE.bam > METHYLOME.tsv command, and every time I only get the header of a methylome.tsv file...

Do you have any tips and tricks that you could share with me?

Best,
Tea

[jts]

This tool is now deprecated as much of the functionality (and much more) can be found in ONT's official tool, modkit

[miki-tesi]

How should modkit be used to prepare data for use with nanomix? In other words, can modkit produce the type of data that nanomix inputs?

[amarkez]

@miki-tesi Have you maybe figured out how to generate the input for nanomix using mbtools (mbtools read-region-frequency) or modkit?