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Published in:
2013 | OriginalPaper | Chapter
MethylCRF, an Algorithm for Estimating Absolute Methylation Levels at Single CpG Resolution from Methylation Enrichment and Restriction Enzyme Sequencing Methods
Authors : Michael Stevens, Jeffrey B. Cheng, Mingchao Xie, Joseph F. Costello, Ting Wang
Published in: Research in Computational Molecular Biology
Publisher: Springer Berlin Heidelberg
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We introduce MethylCRF, a novel Conditional Random Fields-based algorithm to integrate methylated DNA immunoprecipitation (MeDIP-seq) and methylationsensitive restriction enzyme (MRE-seq) sequencing data to predict DNA methylation levels at single CpG resolution. MethylCRF was benchmarked for accuracy against Infinium arrays, RRBS, whole-genome shotgun-bisulfite (WGBS) sequencing and locus specific-bisufite sequencing on the same DNA. MethylCRF transformation of MeDIP/MRE was equivalent to a biological replicate of WGBS in quantification, coverage and resolution, providing a lower cost and widely accessible strategy to create full methylomes.