Table 1. Overview of peaks reported by Graph Peak Caller and MACS2 on A. thaliana for 5 transcription factors (TFs).
Total is the total number of peaks reported by the peak caller, shared is the number of peaks that overlap with a peak from the other peak caller, and unique are peaks reported by one peak caller and not the other. In the categories shared and unique, both the number of peaks with motif match (the number before the /) and the number of peaks found are shown (percent of peaks with motif match are shown in parentheses). All peaks have been trimmed to 120 base pairs around the peak summit (position in peak with lowest q-value), to make the comparison clearer.
| Graph Peak Caller | MACS2 | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Total | Shared | Unique | Total | Shared | Unique | |||||
| ERF115 | 24976 | 3121/21364 | 14.61% | 284/3612 | 7.86% | 23167 | 3108/21364 | 14.55% | 214/1803 | 11.87% |
| SEP3 | 14976 | 989/11982 | 8.25% | 125/2994 | 4.18% | 15517 | 978/11982 | 8.16% | 148/3535 | 4.19% |
| AP1 | 16797 | 764/13405 | 5.70% | 102/3392 | 3.01% | 17030 | 754/13405 | 5.62% | 94/3625 | 2.59% |
| SOC1 | 15502 | 1676/14297 | 11.72% | 116/1205 | 9.63% | 16407 | 1681/14297 | 11.76% | 142/2110 | 6.73% |
| PI | 17518 | 1790/14084 | 12.71% | 300/3434 | 8.74% | 16084 | 1793/14084 | 12.73% | 152/2000 | 7.60% |
| SUM | 89769 | 8340/75132 | 11.10% | 927/14637 | 6.33% | 88205 | 8314/75132 | 11.07% | 750/13073 | 5.74% |