Dear all,
I'm using DiffBind to find the differentially methylated regions. Libraries have been obtained by using the Methyl-binding domain sequencing (MBD-seq). I'm struggling to decide on the best normalization method. Online and in the manual there are some suggestions to deal with ATAC-seq but not with MBD-seq. I wonder if someone has experience with DiffBind and MBD-seq.
Should I go for the background or the Reads in Peak (RiP) normalization? Are there some specific "rules" for the MBD-seq? I know, and it is clearly written in the manual, that there are many strategies and none is the perfect one. But maybe there is someone with more experience than me who can give some hints.
Best
Marianna
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