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

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

  Peak Findera MACS HPeakb 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