Comparison of CpG measurements in RRBS (top) and mRRBS (bottom) across five genomic features. Pie charts compare the relative CpG coverage for different genomic features as sampled by the original RRBS and mRRBS protocol. Twelve representative samples with 10 to 20 million reads and more than 10 million mapped reads were selected from each method (Table 2; Additional file 2). The number of unique CpG measurements residing within a given feature must be observed in at least 80% of the samples used to be scored at a given coverage. Promoters are defined as 1 kb upstream and 1 kb downstream of the transcription start site of Ensembl genes. CgiHunter was used to computationally derive CpG islands with a minimum CpG observed versus expected ratio of 0.6, a minimum GC content of 0.5 and a minimum length of 700 bp. CpG island shores are defined as the 2 kb regions adjacent to the derived CpG islands. Previously published H3K4me2 peaks across multiple human cells were used to derive a consensus enhancer set . As a more global measurement, the genome was divided into non-overlapping consecutive 5 kb tiles, and the number of CpG measurements in each tile was analyzed.
Boyle et al. Genome Biology 2012 13:R92 doi:10.1186/gb-2012-13-10-r92