I have the methylation results from 3 different groups (young, adult, old) that I've processed and have used mcomp to merge ratio files from the same group together and did group comparisons (i.e. young_Vs_adult, adult_Vs_old, young_Vs_old).
I'm looking for a program that will help me find different overlapping DMRs between these group VS group comparisons. Basically I want to see what DMRs are shared or not shared between, for example, young_Vs_adult and adult_Vs_old etc.
It was suggested that I use excel to find overlaps using chr, start, end columns but this seems inefficient and I'm hoping there's another program/module/package that's a better fit for this type of information. Any suggestions?
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You might specify how the data is formatted. If you have
chr start endcolumns, you can usebedtoolsto perform the interval operations.Do not use excel for bioinformatics purposes, using R you could use GRanges objects to find overlaps between your regions : Finding overlaps between GRanges objects