ReviewGenome biology2020
From reads to insight: a hitchhiker's guide to ATAC-seq data analysis.
Review in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 282 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
282 citing papers in PubMed, 1 synthesis or guideline pooled it, 526 citations in OpenAlex.
- Pooled it
- Site-specific programming characterizes dynamic post-translational acetylation of histone H2B lysine 108 in mouse embryonic stem cells.Nature communications · 2026Article
- Chromatin Accessibility Reveals Adaptive Regulatory Variation in a Keystone Freshwater Fish.Molecular ecology · 2026Article
- UnlockingNAR genomics and bioinformatics · 2026Article
- Bridging precision agriculture and human medicine through comparative genetics.Nature reviews. Genetics · 2026Review
- Integrative Epigenomics: Bioinformatics Strategies for Multi-Omics Data Analysis in Health and Disease.Epigenomes · 2026Review
- Article
- Cross-species insights from ART-D to uncover evolutionarily conserved oncogenic mechanisms.Molecular systems biology · 2026Article
- Integrated ATAC-Seq and RNA-Seq Identify ATF3 as a Tumor Suppressor in UVB-Induced Keratinocyte Carcinogenesis.Biology · 2026Article
- Cross-Modal Denoising and Integration of Spatial Multi-Omics Data with CANDIES.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- The cistrome response to hypoxia in human umbilical vein endothelial cells.bioRxiv : the preprint server for biology · 2026Article
- Transcriptional repression by TGIF2 coordinates neurogenic priming and neural stem cell maintenance.Science advances · 2026Article
- NovelbioRxiv : the preprint server for biology · 2026Article
- Ketamine enhances histone H3 (Ser10) phosphorylation via JNK signaling and multi-omics profiling of the hippocampus in a psychotic-like mouse model.Behavioral and brain functions : BBF · 2026Article
- Article
- Truncated Life History Underlies Rapid Local Adaptation in Island Rattlesnake Venom Expression.Genome biology and evolution · 2026Article
- Beyond chromatin accessibility: bulk ATAC-seq as an integrative assay to portray genomes and epigenomes.NAR genomics and bioinformatics · 2026Article
- Benchmarking genome choice in functional genomics analyses.Nature communications · 2026Article
- Heroin addiction modulates transcription factor binding in regulatory regions of the human putamen.Scientific reports · 2026Article
- Epistatic chromatin remodeling during barley response to powdery mildew by ATAC-Seq.Scientific data · 2026Article
222 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
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely used in studying chromatin biology, but a comprehensive review of the analysis tools has not been completed yet. Here, we discuss the major steps in ATAC-seq data analysis, including pre-analysis (quality check and alignment), core analysis (peak calling), and advanced analysis (peak differential analysis and annotation, motif enrichment, footprinting, and nucleosome position analysis). We also review the reconstruction of transcriptional regulatory networks with multiomics data and highlight the current challenges of each step. Finally, we describe the potential of single-cell ATAC-seq and highlight the necessity of developing ATAC-seq specific analysis tools to obtain biologically meaningful insights.
Indexed as
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What OpenQuestion holds
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.