Reconstruction of Diploid High-Order 3D Genome Interactions from Long Noisy Concatemers

The files "IQSEC2_DLR_reads.txt", "IQSEC2_ME_reads.txt", "IQSEC2_bar_data.txt", "RBM3_DLR_reads.txt", "RBM3_ME_reads.txt", and "RBM3_bar_data.txt" contain the data for Figure 7: Haplotype-specific high-order reads plot.The .mcool and .hic files contain diploid contact matrices can be visualized via HiGlass or JuiceBox.Diploid contact matrices used for depicting contact heatmaps (Figures 4B, 5C-G, and 6G; Extended Data Figures 2A,B, 4A-C, 5A-E, and 6), including both Hi-C(paternal.mcool, maternal.mcool) and Pore-C(PoreC_paternal.ds.mcool, PoreC_maternal.ds.mcool, chrX_HP1_hg19_jmatrix_O-Pore-C.hic, chrX_HP2_hg19_jmatrix_O-Pore-C.hic, t_mm_interactions_hg19.hic, t_pp_interactions_hg19.hic) derived matrices.Simulate Pore-C datasets (arab.dpnii.fastq.gz, arab.nlaiii.fastq.gz, dmel.dpnii.fastq.gz, dmel.nlaiii.fastq.gz, human.dpnii.fastq.gz, human.nlaiii.fastq.gz).