QC exclusion criteria reduce noise in methylation signal. The percentage of uniquely aligned reads falling in 500 bp bins containing no CpG dinucleotides pre- and post-QC analysis are plotted as a standard boxplot for samples prior to QC filtering, samples that passed QC, and samples that did not pass QC. An input from a sample that was not subjected to methylation capture is included for reference. The number of samples in each group is included above the baseline. Values for replicate lanes in each group were averaged, and samples were statistically compared using a Wilcoxon rank-sum test. Whiskers indicate 10th and 90th percentiles. 13.5% of 500 bp bins in the genome are classified as CpG barren.
Trimarchi et al. BMC Genomics 2012 13(Suppl 8):S6 doi:10.1186/1471-2164-13-S8-S6