ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization
Byoungkoo Lee, Jiahui Wang, Liuyang Cai, Minji Kim, Sandeep Namburi, Harianto Tjong, Yuliang Feng, Ping Wang, Zhonghui Tang, Ahmed K. Abbas, Chia‐Lin Wei, Yijun Ruan, Sheng Li
Abstract
ChIA-PET (chromatin interaction analysis with paired-end tags) enables genome-wide discovery of chromatin interactions involving specific protein factors, with base pair resolution. Interpretation of ChIA-PET data requires a robust analytic pipeline. Here, we introduce ChIA-PIPE, a fully automated pipeline for ChIA-PET data processing, quality assessment, visualization, and analysis. ChIA-PIPE performs linker filtering, read mapping, peak calling, and loop calling and automates quality control assessment for each dataset. To enable visualization, ChIA-PIPE generates input files for two-dimensional contact map viewing with Juicebox and HiGlass and provides a new dockerized visualization tool for high-resolution, browser-based exploration of peaks and loops. To enable structural interpretation, ChIA-PIPE calls chromatin contact domains, resolves allele-specific peaks and loops, and annotates enhancer-promoter loops. ChIA-PIPE also supports the analysis of other related chromatin-mapping data types.