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MicrobialDarkMatter / nanomotif

Nanomotif - a tool for identifying methylated motifs in metagenomic samples
MIT License
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add support for 4mC motif detection #20

Closed winterlich closed 1 month ago

winterlich commented 3 months ago

Great tool! Would it be possible to integrate motif detection for 4mC and potentially other or even user defined modifications?

SorenHeidelbach commented 3 months ago

Thank you! Currently we do not support it. But it will be integrated soon to support 4mC and any other modification supported by modkit.

Best

ArtRand commented 2 months ago

@SorenHeidelbach

Modkit does support 4mC actually, but there isn't a single-letter code for it page 9 of spec, so you have to use the ChEBI code 21839 instead of a single letter. But if you have a modBAM with 4mC, modkit pileup will work.

SorenHeidelbach commented 2 months ago

Thank you @ArtRand !

We have updated motif_discovery to work with 4mC (#26)

The other modules have not been updated yet to support 4mC, but will shortly

Best Søren!