DNA methylome analysis using short bisulfite sequencing data

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


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • DNA / genetics
  • DNA / metabolism*
  • DNA Methylation*
  • Sequence Analysis, DNA*
  • Sulfites / chemistry*


  • Sulfites
  • DNA