DMAP2: A Pipeline for Analysis of Whole‐Genome‐Scale DNA Methylation Sequencing Data

Abstract DNA methylation is well‐established as a major epigenetic mechanism that can control gene expression and is involved in both normal development and disease. Analysis of high‐throughput‐sequencing‐based DNA methylation data is a step toward understanding the relationship between disease and phenotype. Analysis of CpG methylation at single‐base resolution is routinely done by bisulfite sequencing, in which methylated Cs remain as C while unmethylated Cs are converted to U, subsequently seen as T nucleotides. Sequence reads are aligned to the reference genome using mapping tools that accept the C‐T ambiguity. Then, various statistical packages are used to identify differences in methylation between (groups of) samples. We have previously developed the Differential Methylation Analysis Pipeline (DMAP) as an efficient, fast, and flexible tool for this work, both for whole‐genome bisulfite sequencing (WGBS) and reduced‐representation bisulfite sequencing (RRBS). The protocol described here includes a series of scripts that simplify the use of DMAP tools and that can accommodate the wider range of input formats now in use to perform analysis of whole‐genome‐scale DNA methylation sequencing data in various biological and clinical contexts. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol : DMAP2 workflow for whole‐genome bisulfite sequencing (WGBS) and reduced‐representation bisulfite sequencing (RRBS)