Table 3 Summary of overlaps among peaks identified by different peaking calling algorithms in H3K4me3 and H3K27me3 ChIP-Seq datasets*.
From: HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data
| H3K4me3 | |||||||
|---|---|---|---|---|---|---|---|
| Method (# of peaks) | Peak Finder | MACS | HPeak | Find Peaks | ChIP seeqer | SISSRs | CisGenome |
| Peak Finder (28,960) | 84.3 | 99.8 | 100.0 | 98.2 | 98.0 | 99.6 | |
| MACS (27,568) | 90.6 | 95.4 | 84.8 | 87.7 | 84.8 | ||
| HPeak (41,217) | 99.4 | 100 | 98.9 | 97.1 | |||
| FindPeaks (33,886) | 100 | 99.8 | 100 | ||||
| ChIPseeqer (31,773) | 99.0 | 100 | |||||
| SISSRs (137,286) | 94.6 | ||||||
| CisGenome (46,261) | |||||||
| H3K27me3 | |||||||
| Method (# of peaks) | Peak Finder | MACS | HPeak | Find Peaks | ChIP seeqer | SISSRs | CisGenome |
| Peak Finder (335) | 44.8 | 99.7 | 100 | 77.3 | 90.4 | 70.9 | |
| MACS (1,341) | 42.5 | 42.4 | 23.5 | 24.4 | 32.9 | ||
| HPeak (4,858) | 72.1 | 77.7 | 98.2 | 82.0 | |||
| FindPeaks (8,346) | 77.7 | 91.6 | 87.1 | ||||
| ChIPseeqer (417) | 58.5 | 75.8 | |||||
| SISSRs (2,455) | 25.4 | ||||||
| CisGenome (437) | |||||||