ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization

• DOI: 10.1126/sciadv.aay2078
• Publication Date: 2020-07-10T23:16:47Z
• Authors: Byoungkoo Lee; Jiahui Wang; Liuyang Cai; Minji Kim; Sandeep Namburi; Harianto Tjong; Yuliang Feng; Ping Wang; Zhonghui Tang; Ahmed Abbas; Chia-Lin Wei; Yijun Ruan; Sheng Li
• Keywords: 0303 health sciences; 03 medical and health sciences; JGM; JAXCC; Medicine and Health Sciences; Life Sciences; Research Articles

ChIA-PET (chromatin interaction analysis with paired-end tags) enables genome-wide discovery of chromatin interactions involving specific protein factors, base pair resolution. Interpretation data requires a robust analytic pipeline. Here, we introduce ChIA-PIPE, fully automated pipeline for processing, quality assessment, visualization, and analysis. ChIA-PIPE performs linker filtering, read mapping, peak calling, loop calling automates control assessment each dataset. To enable generates input files two-dimensional contact map viewing Juicebox HiGlass provides new dockerized visualization tool high-resolution, browser-based exploration peaks loops. structural interpretation, calls domains, resolves allele-specific loops, annotates enhancer-promoter also supports the other related chromatin-mapping types.