Calling loops using FitHiChIP, MAPS, and hichipper

We used 5 kb-binned hichipper interactions in GM12878 SMC1A and K562 H3K27ac HiChIP reported by Bhattacharyya et al., 2019²¹ (GM12878 SMC1A from Table_GC-ALL table and K562 H3K27ac from Table_KH-ALL table). MAPS and FitHiChIP (L) interactions (FDR <0.01) were also obtained from Bhattacharyya et al., 2019²¹ (GM12878 SMC1A from Table_GC-ALL table) and interactions, called using pooled replicates, up to 1.5M were used for comparisons.

We ran MAPS (v_1.1.0) for H3K27ac HiChIP in K562 data with HiChIP inferred ChIP peaks (Table Table_KH-L-H from²¹, with the following parameters: “bin_size = 5000; fdr = 0; filter_file = None; generate_hic = 0; mapq = 30; length_cutoff = 1000; threads = 10; per_chr = True, binning_range = 1500000” using pooled allValidPairs file.

We ran FitHiChIP (v_8.1.0) on pooled H3K27ac HiChIP in K562 data with HiChIP inferred ChIP peaks (Table Table_KH-L-H from²¹), with the following parameters: IntType = 3; BINSIZE = 5000; LowDistThr = 5000; UppDistThr = 1500000; UseP2PBackgrnd = 0; BiasType=1; MergeInt=1; QVALUE = 0.01” by providing pooled allValidPairs file.