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Fig. 1 | Genome Biology

Fig. 1

From: Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies

Fig. 1

Data characteristics of ChIA-PET and HiChIP. A PCA plot for replicates of mESC-Smc1 ChIP-seq, ChIA-PET, and HiChIP reads. B PCA plot for replicates of K562-H3K27ac ChIP-seq, ChIA-PET, HiChIP reads. C The count distribution of Mbol restriction enzyme sites across different peak types on 12 HiChIP, 10 ChIA-PET, and 20 ChIP-seq datasets. D The overlap between HiChIP peaks and Mbol restriction sites across 12 HiChIP datasets. E The overlap between ChIP-seq peaks and Mbol restriction sites across 20 ChIP-seq datasets. F The overlap between ChIA-PET peaks and Mbol restriction sites across 10 ChIA-PET datasets. G, H Differential volcano plots comparing ChIP-seq with ChIA-PET and HiChIP peaks quantitatively on 12 HiChIP, 10 ChIA-PET, and 20 ChIP-seq datasets. I Peak co-occupancy between ChIP-seq/ChIA-PET and ChIP-seq/HiChIP on 12 HiChIP, 10 ChIA-PET, and 20 ChIP-seq datasets. Bar plot drawn with standard error bar. ***, p value < 1e−3, p value was calculated by t-test

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