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Table 1 The number of peaks called by different algorithms and at thresholds, and corresponding number of mapped genes

From: Improving ChIP-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information

Method Total number of peaks Number of genes mapped
MACS, p = 1E-8 1,966 996
MACS, p = 1E-5 4,678 2,054
MACS, p = 1E-3 23,306 6,341
T-PIC, p = 1E-3 4,453 1,676
T-PIC, p = 1E-2 6,598 2,318
BayesPeak (PP = 0.90) 15,622 4,495
BayesPeak (PP = 0.70) 21,373 5,507
BayesPeak (PP = 0.5) 27,990 6,533
Union* 38,324 8,057
Intersection* 4,811 2,029
  1. * Union and intersection of the peaks by the three methods, as shown in Figure 1.