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 |