Figure 2

Peak profile benchmark results. Triform outperforms other methods on ChIP-Seq peak profile benchmarks for the TFs NRSF, SRF, and MAX. Coverage, which is the percentage of true peaks recovered in the evaluated regions, is plotted against the false discovery rate (FDR) for each method evaluated. The peak lists from each method are first sorted according to the peak scores from that program. The corresponding coverage and FDR are then calculated as the list is traversed starting at the highest scoring peak. In general, Triform has the lowest FDR for medium-to-high coverage. To emphasize the details at the lower FDR levels, the results from TPic are not shown because of the high FDRs produced by this method. The results from FindPeaks for NRSF are not shown due to the low total number of regions that were recovered (389), giving a total coverage of only 7%.