ArticleGenomics, proteomics & bioinformatics2021
AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis.
Article in Genomics, proteomics & bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
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- Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources.Genome research · 2026Article
- ToxiTaRGET: a multi-omics database for toxicant-responsive molecular targets.Nature communications · 2026Article
- Benchmarking genome choice in functional genomics analyses.Nature communications · 2026Article
- Distinct contributions of Etv2Cell reports · 2026Article
- Contribution of Sex-Biased Expressed Genes in Osteoarthritis.Smart medicine · 2025Article
- Cross-tissue molecular responses in the liver and blood after toxicant exposures.Research square · 2025Article
- Stable characteristics of intrapopulation heterogeneity in virus-specific Th1 cells during chronic viral challenge infection.bioRxiv : the preprint server for biology · 2025Article
- The impact of environmental exposures on the epigenomic and transcriptomic landscape of transposable elements.bioRxiv : the preprint server for biology · 2025Article
- Comprehensive Transcriptomic and Epigenomic Insights into Environmental Toxicant Exposures: The TaRGET II Resource.bioRxiv : the preprint server for biology · 2025Article
- NFIA regulates articular chondrocyte fatty acid metabolism and joint homeostasis.Science translational medicine · 2025Article
- Requirements for the neurodevelopmental disorder-associated gene ZNF292 in human cortical interneuron development and function.Cell reports · 2025Article
- Quantification of single cell-type-specific alternative transcript initiation.bioRxiv : the preprint server for biology · 2025Article
- A narrative review of epigenetic marker in H3K27ac and its emerging potential as a therapeutic target in cancer.Epigenomics · 2025Review
- iPSCs and iPSC-derived cells as a model of human genetic and epigenetic variation.Nature communications · 2025Article
- Stable characteristics of intrapopulation heterogeneity in virus-specific Th1 cells during chronic viral challenge infection.Frontiers in immunology · 2025Article
- Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data.Genomics, proteomics & bioinformatics · 2024Review
- Baf155 controls hematopoietic differentiation and regeneration through chromatin priming.Cell reports · 2024Article
- Defining cis-regulatory elements and transcription factors that control human cortical interneuron development.iScience · 2024Article
Corrections and comments
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Authors and funding
8 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.