megalodon input, which file?

[JWDebler]

Hi, I was just wondering which megalodon output file I should use as input.

I have tried mappings.bam, modified_bases.5mC.bed, mod_mappings.bam and per_read_modified_base_calls.db, but I always get Error in guess_methy_source(element$file) : Format not recognised..

Cheers

[Shians]

You need the tab-delimited output from megalodon which can be produced either by adding --write-mods-text when running or using the megalodon_extras per_read_text modified_bases command after running megalodon.

https://nanoporetech.github.io/megalodon/file_formats.html#per-read-modified-bases

Thanks for asking the question, I will add this into the documentation for future releases.