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Table 3 Summary of overlaps among peaks identified by different peaking calling algorithms in H3K4me3 and H3K27me3 ChIP-Seq datasets*.

From: HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data

H3K4me3
Method (# of peaks) Peak Finder MACS HPeak Find Peaks ChIP seeqer SISSRs CisGenome
Peak Finder (28,960)   84.3 99.8 100.0 98.2 98.0 99.6
MACS (27,568)    90.6 95.4 84.8 87.7 84.8
HPeak (41,217)     99.4 100 98.9 97.1
FindPeaks (33,886)      100 99.8 100
ChIPseeqer (31,773)       99.0 100
SISSRs (137,286)        94.6
CisGenome (46,261)        
H3K27me3
Method (# of peaks) Peak Finder MACS HPeak Find Peaks ChIP seeqer SISSRs CisGenome
Peak Finder (335)   44.8 99.7 100 77.3 90.4 70.9
MACS (1,341)    42.5 42.4 23.5 24.4 32.9
HPeak (4,858)     72.1 77.7 98.2 82.0
FindPeaks (8,346)      77.7 91.6 87.1
ChIPseeqer (417)       58.5 75.8
SISSRs (2,455)        25.4
CisGenome (437)        
  1. * We compare two sets of peaks (generated from two different peak-calling algorithms) to assess how much overlap can be found among them. Numbers displayed is the percentage of peaks in one set that are overlapped with at least one peak in another set. For each pair of peak sets, two percentages can be calculated by switching the order of the two sets. The higher percentage for each pair of peak sets is shown.