Figure 3

Simulation results. (A) An example of the simulated data. The first track shows the assumed binding sites; the following two tracks are the forward and the reverse tag profiles, respectively; and the last track is the binding sites identified by SeqSite. In this case, the assumed binding site coordinates were 500 and 560, and the detected binding sites were at 495 and 558. (B-D) Shown are box-plots of the positions of detected binding sites in different simulated cases. In each panel, the vertical axis represents the genomic position, with red dashed lines showing the true binding locations in the simulation models. Each box-plot shows the results from 100 repeats. (B) Results for single binding site situations. The horizontal axis represents the sequencing depth represented by the number of tags on each strand in the simulated data. (C) Results for two binging sites of distance 60 bp, with different sequencing levels. (D) Results for two binging sites with fixed read count 100. The horizontal axis represents the distance between the two binding sites in the simulation model.