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DNA methylome analysis using short bisulfite sequencing data


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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Figure 1: Effect of bisulfite treatment of DNA.
Figure 2: Performance and accuracy of unbiased base-space and color-space BS-seq alignment tools.
Figure 3: Recommended workflow for the primary analysis of BS-seq data.


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This work was funded by the Biotechnology and Biological Sciences Research Council, UK. A.F. and B.K. received infrastructure support from the Deutsche Forschungsgemeinschaft Excellence Cluster 'Inflammation at Interfaces'.

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Correspondence to Andre Franke or Simon R Andrews.

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The authors declare no competing financial interests.

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Supplementary Figures 1–3 and Supplementary Table 1 (PDF 507 kb)

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Krueger, F., Kreck, B., Franke, A. et al. DNA methylome analysis using short bisulfite sequencing data. Nat Methods 9, 145–151 (2012).

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