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fanglab / nanodisco

nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nanopore sequencing.
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Suitable to compare isogenic methylation profiles? #25

Closed lthomp06 closed 1 year ago

lthomp06 commented 3 years ago

Hello,

I am wondering if nanodisco is a suitable program to compare the methylation patterns of two isogenic strains of E. coli. Would this be possible through the methylation binning of metagenomic contigs functions?

Cheers, Laura

touala commented 3 years ago

Hello Laura,

I don't think I have all the information to respond accurately to your question. I'm assuming you have/want to sequence(d) two isogenic strains of E. coli coming from the same biological sample. If the strains can be assembled in two mostly distinct set of contigs (i.e. enough difference between genome, likely in non-coding regions if they are isogenic), and if the methylation motifs are different (e.g. G6mATC unique to strain A), then yes the methylation binning function should work.

Could you give me more information about the biological context from which the sample comes from? Is it done in an in vitro setup where you mixed strains? Are there other strains/species in the sample?

Regards,

Alan