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PMBio / pycoMeth

DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets
https://pmbio.github.io/pycoMeth/
GNU General Public License v3.0
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Plans to make pycoMeth compatible with Modkit bedMethyl format? #10

Closed bernardo-heberle closed 3 weeks ago

bernardo-heberle commented 9 months ago

Hello,

Because of the improvements in modified basecalling accuracy Nanopolish states that it does not support R10 flowcells on its GitHub. It also seems that Oxford Nanopore is investing in this new tool suite called Modkit for analysis of base modification. I was wondering if there are any plans for pycoMeth to start supporting the bedMethyl files created by the pileup function from modkit? Alternatively, do you know of a way to convert the bedMethyl files from modkit into the MetH5 format from Nanopolish so that they are compatible with pycoMeth?

I really like the ease of use and great features included in pycoMeth. It would be great to be able to easily integrate it with the new R10 data pre-processed using modkit.

SkabbiVML commented 8 months ago

Hi

I came here with the same question, doesn't look like there is an answer to this yet. @bernardo-heberle , have you found a way to perform differential methylation analysis on data generated via R10 flow-cells and modkit?

Cheers

Skabbi

bernardo-heberle commented 8 months ago

Hi Skabbi,

I got no answer for this. It looks like modkit does have a module for differential methylation analysis in their documentation under 1.11. Perform differential methylation scoring - https://nanoporetech.github.io/modkit/intro_dmr.html. You could use that and then generate the visualization for the results on your own. That is what I am planning on doing.

I have not had the time to dig deep into this yet, if I find a way to make the output from modkit compatible with pycoMeth I will post an update here. But to be honest that is pretty low on my priority list right now so it might be a while.

Cheers, Bernardo

SkabbiVML commented 8 months ago

Hei, thanks for the reply @bernardo-heberle! The modkit documentation is offline atm but I'll keep it in mind and hope to try.

Thanks again

Skabbi