General Information
| Description | Consistent simultaneous estimates of DNA methylation and hydroxymethylation |
| Homepage | http://smithlab.usc.edu/software/mlml |
Publications
MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation
Motivation:
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.
Results:
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.
Availability:
http://smithlab.usc.edu/software/mlml
Contact:
andrewds@usc.edu
Supplementary information:
Supplementary material is available at Bioinformatics online.
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