DNA methylation and nucleosome positioning are two key mechanisms that 
contribute to the epigenetic control of gene expression. During carcinogenesis, 
the expression of many genes is altered alongside extensive changes in the 
epigenome, with repressed genes often being associated with local DNA 
hypermethylation and gain of nucleosomes at their promoters. However the 
spectrum of alterations that occur at distal regulatory regions has not been 
extensively studied. To address this we used Nucleosome Occupancy and 
Methylation sequencing (NOMe-seq) to compare the genome-wide DNA methylation and 
nucleosome occupancy profiles between normal and cancer cell line models of the 
breast and prostate. Here we describe the bioinformatic pipeline and methods 
that we developed for the processing and analysis of the NOMe-seq data published 
by (Taberlay et al., 2014 [1]) and deposited in the Gene Expression Omnibus with 
accession GSE57498.