Fig. 1.

Overview and different settings/parameters of FitHiChIP pipeline. a Overview of FitHiChIP pipeline. b Comparison of different normalization techniques versus no normalization for FitHiChIP in terms of recovering loops from PCHiC data on the same cell type. c Recovery performance of PCHiC loops using different settings and window sizes for our merging filter (M) technique. d Recovery of ChIP-seq peaks by MACS2 peaks inferred from HiChIP data using different sets of reads. e Comparison of the choice of peak calls (either from a reference ChIP-seq data or inferred from HiChIP data directly) in terms of recovering a reference set of loop calls from GM12878 Hi-C data. The symbol N indicates total number of loops (or peaks) for the corresponding method. Source data are provided as a Source Data file