Analysing and interpreting DNA methylation data

By Christoph Bock. Nature reviews genetics, 2012

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Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics (2015, methodology): “Alignment was done with the Bismark Bisulﬁte Mapper (Krueger and Andrews, 2011),whichisathree-letterbisulﬁtealignerthatusesaninsilicobisulﬁte-con-verted reference genome (Bock, 2012).”
A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package. (2014, unknown): “From a technological perspective, MeRIP-Seq can be considered a marriage of three relatively well-studied techniques: ChIP-Seq [6, 7], RNA-Seq [8, 9] and MeDIP-Seq [10, 11], yet it brings new computational challenges not addressed previously [12].”
A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics (2013, background): “Users may also use alternative mappers (see [14] and [15] for reviews).”