Differential methylation analysis for bisulfite sequencing using DSS

• Authors: Hao Feng, Emory University; Hao Wu, Emory University
• Journal Title: Quantitative Biology
• Volume: Volume 7, Number 4
• Publisher: Higher Education Press | 2019-12-01, Pages 327-334
• Type of Work: Article | Post-print: After Peer Review
• Publisher DOI: http://doi.org/10.1007/s40484-019-0183-8
• Subjects: Biology, Biostatistics
• Keywords: DNA methylation; bisulfite sequencing; differential methylation; epigenetics

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.