Title

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

Document Type

Article

Publication Date

7-1-2020

Keywords

JGM, JAXCC

JAX Source

Sci Adv 2020 Jul 10; 6(28):eaay2078

PMID

32832596

DOI

https://doi.org/10.1126/sciadv.aay2078

Grant

HG009409,GM133562,CA034196

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.

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