running modkit dmr after `epi2me-labs/wf-human-variation` pipeline using mod

[Sepideh89]

Hi,

I ran my samples using the epi2me-labs/wf-human-variation pipeline using mod, and I obtained .bedmethyl files as the output.

Now I’d like to run modkit dmr for differential analysis. Do I still need to run modkit pileup before using modkit dmr, or can I directly use the .bedmethyl files generated by the epi2me workflow?

Thanks in advance for your help!

Best,

[ArtRand]

Hello @Sepideh89,

You do not need to re-run pileup if you have one .bedmethyl file for each condition you want to test. For example, if you want to compare two samples you need the .bedmethyl from each. If you want to compare between haplotypes for a single sample, you need a .bedmethyl for each haplotype.

If the .bedmethyl files have not been bgzip compressed and tabix indexed, you'll need to do those steps first. There is more documentation here.

[Sepideh89]

Thanks for your response!