How to identify CG, CHG, or CHH from MeDIP data
We have data generated using EpiXplore Meth-Seq DNA Enrichment Kit on Novaseq 6000. It is basically for one of the non-model plant species. We have 3 replicates for each group. Now we require to identify differently methylated regions and its differentiation into CG, CHG, or CHH from MeDIP data. Kindly suggest some software for getting required information.
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I know that CpG types can be identified using whole genome bisulphite data. But could it be possible using MeDIP data too? We tried using QSEA for analysis but could not find all 3 types of CpGs.
I am in a urgent need to get information about CG, CHG, or CHH sites from MeDIP data. Any help is appreciated.