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Table 1 F1-score and run-time of competing peak callers on H3K4me3 and H3K36me3 benchmark region detection using ENCODE ChIP-seq datasets

From: ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach

Cell line K562 GM12878
Histone protein H3K4me3 H3K36me3 H3K4me3 H3K36me3
F1-score (Supervised)
 ChIP-BIT2 0.93 0.90 0.95 0.90
 MACS2 0.89 0.78 0.93 0.83
 CNN-peaks 0.91 0.85 0.90 0.88
F1- score (unsupervised)
 ChIP-BIT2 0.88 0.82 0.91 0.82
 MACS2 0.82 0.77 0.84 0.79
Run-time (unsupervised)
 ChIP-BIT2 14m1s 9m21s 15m7s 9m9s
 MACS2 3m42s 2m39s 5m35s 2m32s