BMC Bioinformatics

Table 2 Numbers of peaks and length distributions reported by various peak-calling programs

From: PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci

Program	Peaks	Length
		min	Q1	Median	Mean	Q3	Max
FindPeaks ^†	38837	301	821	1189	1379	1725	24970
SWEMBL	33475	100	296	381	429	494	8669
MACS ^‡	9818	113	308	380	407	477	5983
ChIPSeqMini	4019	38	200	278	300	375	1291
SISSRs ^‡	3498	40	40	60	82	100	640
USeq ^∓	979	109	207	261	273	318	1521

^† Minimum peak height = 5
^‡ P-value < 1e^-5
^∓FDR 1%, fold change = 2
ChIP-seq data for Oct4 [12] were analyzed using six different peak callers. The numbers of peaks identified by each method along with the respective length distributions are listed.

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ISSN: 1471-2105

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