Interactive visualization of ChIA-PET 2D contact maps using Juicebox.js and HiGlass. ChIA-PIPE uses Juicebox.js and HiGlass to visualize ChIA-PET data in 2D contact maps. After the duplications are removed and the uniquely mapped PETs are retained, the BAM file can be converted to a merged_nodups.txt file and used as input to the Juicer tool Pre command, creating a .hic file. Loops called by ChIA-PIPE can also be visualized in Juicebox by representing them in the appropriate text file format, which is analyzed using the data processing tool termed Juicer (26). Juicer generates a contact matrix file (.hic), which is in a highly compressed binary file format and can be accessed by Juicebox (27) visualization software. These tools were initially developed to visualize Hi-C data, and we adopted them to process and visualize our ChIA-PET 2D contact maps. ChIA-PIPE uses Juicer to generate the contact matrix file for 10 different resolutions (2.5 Mb, 1 Mb, 500 kb, 250 kb, 100 kb, 50 kb, 25 kb, 10 kb, 5 kb, and 1 kb), and thus, users can easily adjust multiscale genomic regions from an all-chromosomes view to a view of a specific genomic region up to 1-kb resolution. The chromatin contact matrix is based on the adjustable resolution, from a bin size of 2.5 Mb × 2.5 Mb to 1 kb × 1 kb. The contact matrix contains the total contact count within the specific genomic bin. Contact signal intensity or counts are represented by the intensity of red color in default, from low contact (light red) to high contact (dark red). The default color can be changed by user. Four different normalization methods (none, coverage, coverage_sqrt, and balanced) can be applied to the contact heat map data to remove technical noise or adjust biased signal.

BASIC Browser for interactive, high-resolution visualization of ChIA-PET loops, domains, and binding coverage. ChIA-PIPE uses an in-house–developed genome browser to visualize the binding peaks and chromatin loops (Fig. 3B). The chromatin interaction data file (loop.gz; Fig. 1B.2) is uploaded to the BASIC Browser and displays chromatin contacts as arcs between the two genomic loci for each loop. The length of an arc indicates the linear genomic distance of a loop, and the height of an arc reflects the contact frequency (PET counts) detected in the ChIA-PET data. BASIC Browser enables the visualization of the binding peaks and demarcates the summit of binding sites from the protein-binding profile data (.bedgraph) (Fig. 1B.3). In addition, allele-specific files for binding peaks and chromatin interactions (Fig. 1B.4) are also visualized. The advantages of using browser-based visualization includes detailed bp resolution presentation of chromatin loops, in relation to protein-binding peaks, and the capacity to integrate these data with other genome browser information on other experimental data (e.g., RNA-seq, ChIP-seq, and ATAC-seq).

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