This is a useful paper from 2017 titled Strategies for analyzing bisulfite sequencing data. It reviews sequencing and alignment approaches, general methylome analysis, differential methylation and annotation, as well as recommending analysis platforms for non-coders. Section 4.1 discusses differential methylation methods, comparing three different methods using a simulated dataset, including as a subset of one method … Continue reading On the optimal use of methylKit
Category: methylation
Permute? or no?
This post covers brief findings from exploring permutation tests when looking for differentially methylated genes from whole genome bisulfite sequencing. The idea behind it: if we randomly shuffle the data between control and treatment samples and see roughly the same number of genes coming out as differentially methylated then we can't say the genes we originally … Continue reading Permute? or no?
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