Differential methylation analysis for bisulfite sequencing using DSS

• Type of Material: Article
• Authors: Hao Feng, Emory University; Hao Wu, Emory University
• Language: English
• Date: 2019-12-01
• Publisher: Higher Education Press
• Publication Version: Author Accepted Manuscript (After Peer Review)
• Copyright Statement: © The Author(s) 2019.
• License: Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1007/s40484-019-0183-8
• Title of Journal or Parent Work: Quantitative Biology
• Volume: 7
• Issue: 4
• Start Page: 327
• End Page: 334
• Keywords: epigenetics; DNA methylation; differential methylation; bisulfite sequencing

Abstract

Bisulfite sequencing (BS-seq) technology measures DNA methylation at single nucleotide resolution. A key task in BS-seq data analysis is to identify differentially methylation (DM) under different conditions. Here we provide a tutorial for BS-seq DM analysis using Bioconductor package DSS. DSS uses a beta-binomial model to characterize the sequence counts from BS-seq, and implements rigorous statistical method for hypothesis testing. It provides flexible functionalities for a variety of DM analyses.