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 |