AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis
- Author:
Liu SHAOPENG
1
;
Li DAOFENG
;
Lyu CHENG
;
M.Gontarz PAUL
;
Miao BENPENG
;
A.F.Madden PAMELA
;
Wang TING
;
Zhang BO
Author Information
1. Department of Developmental Biology,Center of Regenerative Medicine,Washington University School of Medicine,St.Louis,MO 63108,USA
- Keywords:
ATAC-seq;
Quality control;
Chromatin accessibility;
Differential analysis;
Data visualization
- From:
Genomics, Proteomics & Bioinformatics
2021;19(4):641-651
- CountryChina
- Language:Chinese
-
Abstract:
Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) is a technique widely used to investigate genome-wide chromatin accessibility. The recently published Omni-ATAC-seq protocol substantially improves the signal/noise ratio and reduces the input cell number. High-quality data are critical to ensure accurate analysis. Several tools have been developed for assessing sequencing quality and insertion size distribution for ATAC-seq data;however, key quality control (QC) metrics have not yet been established to accurately determine the quality of ATAC-seq data. Here, we optimized the analysis strategy for ATAC-seq and defined a series of QC metrics for ATAC-seq data, including reads under peak ratio (RUPr), background (BG), promoter enrichment (ProEn), subsampling enrichment (SubEn), and other measurements. We incorporated these QC tests into our recently developed ATAC-seq Integrative Analysis Package (AIAP) to provide a complete ATAC-seq analysis system, including quality assurance, improved peak calling, and downstream differential analysis. We demonstrated a significant improvement of sensitivity (20％–60％) in both peak calling and differential analysis by processing paired-end ATAC-seq datasets using AIAP. AIAP is compiled into Docker/Singularity, and it can be executed by one command line to generate a comprehensive QC report. We used ENCODE ATAC-seq data to benchmark and generate QC recommendations, and developed qATACViewer for the user-friendly interaction with the QC report. The software, source code, and documentation of AIAP are freely available at https://github.com/Zhang-lab/ATAC-seq_QC_analysis.
