Figure 5.

Visualizing differential methylation events. (a) Horizontal bar plots show the number of hyper- and hypomethylation events per chromosome, as a percent of the sites with the minimum coverage and differential. By default this is a 25% change in methylation and all samples with 10X coverage. (b) Example of bedgraph file uploaded to UCSC browser. The bedraph file is for differentially methylated CpGs with at least a 25% difference and q-value <0.01. Hyper- and hypo-methylated bases are color coded. The bar heights correspond to % methylation difference between ER+ and ER- sets. ER+, estrogen receptor-alpha expressing; ER-, estrogen receptor-alpha non-expressing. UCSC, University of California Santa Cruz.