Thank you, for the amazing tool, I have 9 bedmethyl files(4 control and 5 disease cases), these files generated from modkit tool. I have some questions

[ralanany]

1- I want to make differential methylation anlysis between these samples, I thought I should use that command mentioned in the tutorial

modkit dmr multi
-s ${norm_pileup_1}.gz norm1
-s ${tumor_pileup_1}.gz tumor1
-s ${norm_pileup_2}.gz norm2
-s ${tumor_pileup_2}.gz tumor2
-o ${dmr_dir} \ # required for multi -r ${cpg_islands} \ # skip this option to perform base-level DMR --ref ${ref}
--base C
-t 10
-f
--log-filepath dmr_multi.log

Am I right?. If yes, How can I determine the most significant differentially methylated cpgs?

2- I have betas from HM-450 micro-array for the same samples, How can I find correlation between values from microarray and from ont analysis?

3-To my knowledge ONT don't give betavalues like that produced from array analysis, which value is corresponding to the betavalue, to be able to draw TSNE or UMAP for group discrimination and dimensonality reduction?

Sorry for disturbance and appreciate your kind reply

[ArtRand]

Hello @ralanany.

The Modkit command you've found is correct for performing differential methylation on multiple samples. You can use the score column or if you want to perform single-site analysis or segmentation you can use map_pvalue as a ranking.

I don't have any advice on how to directly compare to beta values from array data, but I'm looking into it - I'll let you know.