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Fig. 2 | BMC Bioinformatics

Fig. 2

From: DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data

Fig. 2

DMRfinder analyzes novel CpG sites. a A segment of chromosome 1 in a CEBPB binding site, as shown with the UCSC genome browser [12]. The canonical sequence has three CpG sites (blue boxes, #1, 3, and 4). The deletion of the adenine at position 21,741,341, a known variant (rs11348696) results in the creation of a novel CpG site (red box, #2). b The alignment of the methylation strings of six reads from the IMR90 replicate 1 dataset with the genomic segment in part A. The methylation strings show only CpG methylation status (‘z’ = unmethylated, ‘Z’ = methylated). All six reads have a deletion of the adenine at position 21,741,341 (‘-’), and thus indicate that the methylation status occurs in a CpG context. c With Bismark, the output summarizing methylation counts lists data for sites #1, 3, and 4, but omits the new CpG site. d With DMRfinder, the output includes the novel CpG site, revealing a higher methylation level in this genomic region

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