Ruan Lab ChIA-PIPE Pipeline

Status: released
Title: Ruan Lab ChIA-PIPE Pipeline
Assays: ChIA-PET
Description: ChIA-PIPE is 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.
Lab: Yijun Ruan, JAX
Award PI: Yijun Ruan, JAX
Source: http://github.com/TheJacksonLaboratory/ChIA-PIPE

Description: Ruan Lab ChIA-PIPE processing pipeline for ChIA-PET data