title: DNA methylome analysis using short bisulfite sequencing data.
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.
authors.affiliation: Bioinformatics Group, The Babraham Institute, Cambridge, UK.
authors.forename: Felix
authors.initials: F
authors.lastname: Krueger
authors.forename: Benjamin
authors.initials: B
authors.lastname: Kreck
authors.forename: Andre
authors.initials: A
authors.lastname: Franke
authors.forename: Simon R
authors.initials: SR
authors.lastname: Andrews
mesh_terms: D004247:DNA / Q000235:genetics / Q000378:metabolism*; D019175:DNA Methylation; D017422:Sequence Analysis, DNA; D013447:Sulfites / Q000737:chemistry*
chemical_list: D013447:Sulfites; D004247:DNA