EM-Seq of tumor and non-tumor samples from radical prostatectomy specimens

Files with .markdup.sorted_CpG.bw suffix correspond to individual samples and were generated as follow: BedGraph files of the CpG positions on the hg19 genome assembly were generated using nf-core/methylseq pipeline. The first four columns of the Bedgraph containing the coordinates of the loci and the mean methylation values methylation level for each loci were extracted and converted to BigWig format with UCSC BedGraphToBigWig. Even numeric ids correspond to non-tumor samples and their next odd ids correspond to their paired tumor sample. mu1.bw corresponds to the mean methylation for the tumor group. mu2.bw corresponds to the mean methylation for the non-tumor group. diff.bw corresponds to the mean difference tumor - non-tumor group. pmlog10fdr.bw corresponds to the -log10(FDR + 1e-30) where FDR is the adjusted p-value computed from the DSS package.