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. 2019 Feb 19;15(2):e1006731. doi: 10.1371/journal.pcbi.1006731

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%