Motivation: 5-Methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are important epigenetic regulators of gene expression. 5mC and 5hmC levels can be computationally inferred at single base resolution using sequencing or array data from paired DNA samples that have undergone bisulfite and oxidative bisulfite conversion. Current estimation methods have been shown to produce irregular estimates of 5hmC level or are extremely computation intensive.
Results: We developed an efficient method oxBS-MLE based on binomial modeling of paired bisulfite and oxidative bisulfite data from sequencing or array analysis. Evaluation in several datasets showed that it outperformed alternative methods in estimate accuracy and computation speed.
Availability and implementation: oxBS-MLE is implemented in Bioconductor package ENmix.
Contact: niulg@ucmail.uc.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US.