Fig. 11

Peak calling performance on Maize Epigenomics B73V3 nuprime Buckler Shoot DNS-seq data. Top browser window (a) shows the biological range Chr1: 2,730,000–2,810,000. Bottom window (b) is another range Chr1: 1,745,000–1,760,000 on a larger scale. In each window, from top to bottom: first signal track is light digestion group (treatment, color = blue); second signal track is heavy digestion group (control, color = red); Third signal track is difference track (light minus heavy, color code: positive = blue, negative = red). Segment tracks are enriched regions called by: iSeg-neg(a): iSeg calls of negative regions on the difference track with bc = 1.0; iSeg-neg(b): iSeg calls of negative regions on the difference track with bc = 2.0; iSeg-neg(c): iSeg calls of negative regions on the difference track with bc = 3.0; iSeg-pos(a): iSeg calls of positive regions on the difference track with bc = 1.0; iSeg-pos(b): iSeg calls of positive regions on the difference track with bc = 2.0; iSeg-pos(c): iSeg calls of positive regions on the difference track with bc = 3.0; MACS(a): MACS calls with light as treatment and heavy as control, FDR = 0.05; MACS(b): MACS calls with light as treatment and heavy as control, FDR = 0.01; MACS(c): MACS calls with light as treatment and heavy as control, FDR = 0.001; SICER(a): SICER calls with light as treatment and heavy as control, window size = 20 and gap size = 40; SICER(b): SICER calls with light as treatment and heavy as control, window size = 30 and gap size = 60; SICER(c): SICER calls with light as treatment and heavy as control, window size = 50 and gap size = 100; PePr(a): PePr calls with light as treatment and heavy as control, broad peak mode; PePr(b): PePr calls with light as treatment and heavy as control, sharp peak mode