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

BMC Bioinformatics

Table 2 Summary of peaks identified by various peaking calling algorithms.

	Peak Finder^a	MACS	HPeak^b	FindPeaks	HPeak (chip only)	ChIPseeqer (control)	SISSRs	CisGenome
NRSF
chip: 1.7M
mock: 2.3M
Number of peaks	1,935	4,679	4,404	3,445	4,085	2,361	5,243	2,545
Covered space (kb)	908	1,902	1,112	4,936	1,512	682	276	775
Avg peak width (bp)	469	406	253	1,433	370	289	53	304
STAT1
stimulated: 15.3M
unstimulated: 13.0M
Number of peaks	-	22,402	24,490	41,127	43,443	11,662	9,561	38,878
Covered space (kb)	-	16,940	6,562	46,781	15,354	3,025	455	10,012
Avg peak width (bp)	-	756	269	1,137	353	259	48	258
H3K4me3
16.8M
Number of peaks	28,960	27,568	-	33,890	41,217	31,773	137,286	46,261
Covered space (kb)	30,610	36,675	-	83,348	30,435	18,789	6,464	26,500
Avg peak width (bp)	1,057	1,330	-	2,459	738	591	47	573
H3K27me3
9.0M
Number of peaks	335	1,342	-	8,348	4,858	417	2,458	437
Covered space (kb)	83	607	-	19,234	894	115	138	191
Avg peak width (bp)	248	452	-	2304	184	276	56	436

ISSN: 1471-2105