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nanoporetech / modkit

A bioinformatics tool for working with modified bases
https://nanoporetech.com/
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Contig names source #213

Closed Ge0rges closed 1 week ago

Ge0rges commented 1 week ago

Hi Art,

I was wondering where does modkit get the contig name for the bedmethyl outputs of pileup? I'm encountering an odd issue where one of the contigs output doesn't exist in the reference file under the same name. But there might be more at play here than a bug in modkit.

ArtRand commented 1 week ago

Hello @Ge0rges,

The contig names come from the header in the modBAM (@SQ lines). Whatever reference you use to align the reads needs to be carried through downstream steps.

Ge0rges commented 1 week ago

@ArtRand does it make sense that modkit dmr multi, modkit dmr pair or modkit find-motifs complete successfully if there is no overlap between contig names in the .fna and the and the bedmethyl?