Table 3

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

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)


* 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.

Qin et al. BMC Bioinformatics 2010 11:369   doi:10.1186/1471-2105-11-369

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