Introduction

The two major epigenetic modifications of cytosines, 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC), coexist with each other in a range of mammalian cell populations. Increasing evidence points to important roles of 5-hmC in demethylation of 5-mC and epigenomic regulation in development. Recently developed experimental methods allow direct single-base profiling of either 5-hmC or 5-mC. Meaningful analyses seem to require combining these experiments with bisulfite sequencing, but doing so naively produces inconsistent estimates of 5-mC or 5-hmC levels.We present a method to jointly model read counts from bisulfite sequencing, oxidative bisulfite sequencing and Tet-Assisted Bisulfite sequencing, providing simultaneous estimates of 5-hmC and 5-mC levels that are consistent across experiment types.http://smithlab.usc.edu/software/mlml

Publications

  1. MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation.
    Cite this
    Qu J, Zhou M, Song Q, Hong EE, Smith AD, 2013-10-01 - Bioinformatics (Oxford, England)

Credits

  1. Jianghan Qu
    Developer

    Molecular and Computational Biology, University of Southern California, United States of America

  2. Meng Zhou
    Developer

  3. Qiang Song
    Developer

  4. Elizabeth E Hong
    Developer

  5. Andrew D Smith
    Investigator

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Summary
AccessionBT000022
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByAndrew D Smith