DNA methylome analysis using short bisulfite sequencing data
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Updated: May 25, 2026

Targeted DNA Methylation Analysis by Next-generation Sequencing
Published on: February 24, 2015
Felix Krueger1, Benjamin Kreck, Andre Franke
1Bioinformatics Group, The Babraham Institute, Cambridge, UK.
Abstract:
Bisulfite conversion of genomic DNA combined with next-generation sequencing (BS-seq) is widely used to measure the methylation state of a whole genome, the methylome, at single-base resolution. However, analysis of BS-seq data still poses a considerable challenge. Here we summarize the challenges of BS-seq mapping as they apply to both base and color-space data. We also explore the effect of sequencing errors and contaminants on inferred methylation levels and recommend the most appropriate way to analyze this type of data.
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