DNA methylome analysis using short bisulfite sequencing data.

Authors:
Felix Krueger, Benjamin Kreck, Andre Franke, Simon R Andrews
Year of publication:
2012
Volume:
9
Issue:
2
Issn:
1548-7091
Journal title abbreviated:
NAT METHODS
Journal title long:
Nature methods
Impact factor:
25.328
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.