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cultivarium / MicrobeMod

A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
MIT License
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Significance of identified motifs? #20

Closed starkeynight closed 4 months ago

starkeynight commented 4 months ago

Hello,

I am curious about the outputs from call_methylation. Are identified motifs determined based on a pre-set list of possible motifs, or are they identified based simply on the sequences? (I.e. - is this de novo methylation motif detection?)

If available, it would be useful to know if there is a list of possible methylation motifs that can be detected.

Thanks!

alexcritschristoph commented 4 months ago

I have good news for you: all motifs are identified de novo from the methylated sites. There is no apriori list, only rules are they have to be between 3 and 26 bp long.

starkeynight commented 4 months ago

Fantastic! Thank you very much :)