ArticleCell systems2020
Quantification, Dynamic Visualization, and Validation of Bias in ATAC-Seq Data with ataqv.
Article in Cell systems, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
62 citing papers in PubMed.
- Androgen receptor drives divergent chromatin accessibility programs in benign and malignant prostate epithelial cells.Nucleic acids research · 2026Article
- Chromatin topology and distal elements underlie divergent cell-type-specific regulation of 9p21 locus cell cycle genes.Cell genomics · 2026Article
- Transcriptomic and regulatory landscape of liver tissue associated with meat and carcass quality traits in cattle.Journal of animal science and biotechnology · 2026Article
- Article
- Scalable hypothalamic neuron differentiation from human pluripotent stem cells suitable for modeling metabolic disorders.Stem cell reports · 2026Article
- Epigenetic landscape, key transcriptional regulators, and in vivo identification of human Tr1 cells.Science advances · 2026Article
- Genetic demultiplexing and transcript start site identification from nanopore sequencing of 10x Genomics multiome libraries.bioRxiv : the preprint server for biology · 2026Article
- Ring finger protein 213 regulates B-cell receptor signaling, metabolism, and development in B lymphocytes.Signal transduction and targeted therapy · 2026Article
- Donor-matched iPSC model reveals context-dependent T2D genetic signals in fibro-adipogenic progenitors.bioRxiv : the preprint server for biology · 2026Article
- Liver single-nucleus multiome profiling reveals cell-type mechanisms for cardiometabolic traits.American journal of human genetics · 2026Article
- The neuronal chromatin landscape in brains from individuals with schizophrenia is linked to early fetal development.Nature neuroscience · 2025Article
- Integrative multi-omics uncovers skeletal muscle enhancer programming of cardiorespiratory fitness.bioRxiv : the preprint server for biology · 2025Article
- Epigenetic Histone β-Hydroxybutyrylation Contributes to Renoprotection by β-Hydroxybutyrate in the Dahl Rat.Hypertension (Dallas, Tex. : 1979) · 2025Article
- PEAKQC: periodicity evaluation in single-cell ATAC-seq data for quality assessment.Briefings in bioinformatics · 2025Article
- Chromatin accessibility provides a window into the genetic etiology of human brain disease.Trends in genetics : TIG · 2025Review
- Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits.Genome research · 2025Article
- Growth of human regulatory CD4iScience · 2025Article
- Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma.Blood cancer discovery · 2025Article
- The transcription factor Traffic jam orchestrates the somatic piRNA pathway in Drosophila ovaries.Cell reports · 2025Article
- Reducing batch effects in single cell chromatin accessibility measurements by pooled transposition with MULTI-ATAC.bioRxiv : the preprint server for biology · 2025Article
2 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) has become the preferred method for mapping chromatin accessibility due to its time and input material efficiency. However, it can be difficult to evaluate data quality and identify sources of technical bias across samples. Here, we present ataqv, a computational toolkit for efficiently measuring, visualizing, and comparing quality control (QC) results across samples and experiments. We use ataqv to analyze 2,009 public ATAC-seq datasets; their QC metrics display a 10-fold range. Tn5 dosage experiments and statistical modeling show that technical variation in the ratio of Tn5 transposase to nuclei and sequencing flowcell density induces systematic bias in ATAC-seq data by changing the enrichment of reads across functional genomic annotations including promoters, enhancers, and transcription-factor-bound regions, with the notable exception of CTCF. ataqv can be integrated into existing computational pipelines and is freely available at https://github.com/ParkerLab/ataqv/.
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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.