BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions
- Equal contributors
1 Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
2 Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Genome Biology 2012, 13:R83 doi:10.1186/gb-2012-13-10-r83Published: 3 October 2012
DNA methylation is an important epigenetic modification involved in gene regulation, which can now be measured using whole-genome bisulfite sequencing. However, cost, complexity of the data, and lack of comprehensive analytical tools are major challenges that keep this technology from becoming widely applied. Here we present BSmooth, an alignment, quality control and analysis pipeline that provides accurate and precise results even with low coverage data, appropriately handling biological replicates. BSmooth is open source software, and can be downloaded from http://rafalab.jhsph.edu/bsmooth webcite.