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
Volume
6
Issue
28
First Page
2078
Last Page
2078
ISSN
2375-2548
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.
Recommended Citation
Lee B,
Wang J,
Cai L,
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Namburi S,
Tjong H,
Feng Y,
Wang P,
Tang Z,
Abbas A,
Wei C,
Ruan Y,
Li S.
ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization. Sci Adv 2020 Jul 10; 6(28):eaay2078