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

DNA methylome analysis using short bisulfite sequencing data

Felix Krueger  1 , Benjamin Kreck, Andre Franke, Simon R Andrews
Affiliations
Review

DNA methylome analysis using short bisulfite sequencing data

Felix Krueger et al. Nat Methods. .

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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References

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    1. Nat Methods. 2010 Feb;7(2):133-6 - PubMed
    1. Nat Protoc. 2011 Apr;6(4):468-81 - PubMed
    1. Nature. 2009 Nov 19;462(7271):315-22 - PubMed
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