Approaches for the analysis and interpretation of whole genome bisulfite sequencing data

Tim Stuart, Sam Buckberry, Ryan Lister

Research output: Chapter in Book/Conference paperChapterpeer-review

6 Citations (Scopus)


DNA methylation is a covalent modification of DNA that plays important roles in processes such as the regulation of gene expression, transcription factor binding, and suppression of transposable elements. The use of whole genome bisulfite sequencing (WGBS) enables the genome-wide identification and quantification of DNA methylation patterns at single-base resolution and is the gold standard for analysis of DNA methylation. Computational analysis of WGBS data can be particularly challenging, as many computationally intensive steps are required. Here, we outline a step-by-step approach for the analysis and interpretation of WGBS data. First, sequencing reads must be trimmed, quality checked, and aligned to the genome. Second, DNA methylation levels are estimated at each cytosine position using the aligned sequence reads of the bisulfite treated DNA. Third, regions of differential cytosine methylation between samples can be identified. Finally, these data need to be visualized and interpreted in the context of the biological question at hand. © Springer Science+Business Media, LLC 2018.

Original languageEnglish
Title of host publicationEpigenome Editing
Subtitle of host publicationMethods and Protocols
EditorsAlbert Jeltsch, Marianne G. Rots
Place of PublicationNew York
Number of pages12
ISBN (Electronic)9781493977741
ISBN (Print)9781493977734
Publication statusPublished - 2018

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


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