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Nat Methods. 2012 Jan 30;9(2):145-51. doi: 10.1038/nmeth.1828.

DNA methylome analysis using short bisulfite sequencing data.

Author information

1
Bioinformatics 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.

PMID:
22290186
DOI:
10.1038/nmeth.1828
[Indexed for MEDLINE]

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