Table 2

Summary of peaks identified by various peaking calling algorithms.

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


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

Open Data