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BEDTools: a flexible suite of utilities for comparing genomic features
Open accessAbstract
MOTIVATION: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner. RESULTS: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets. AVAILABILITY AND IMPLEMENTATION: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools CONTACT: aaronquinlan@gmail.com; imh4y@virginia.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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“Peaks present in mock experiments were then subtracted with bedtools (Quinlan and Hall 2010), and the peak set was converted from BED to SAF format.”
From Mitochondrial retrograde control of transcription evolves with respiratory stress, metabolic adaptation, and virulence in budding yeasts (2026) · cites this paper as Quinlan and Hall 2010
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“Generation of consensus peak files from multiple biological replicates was performed using bedtools intersect”
From Super-enhancers include classical enhancers and facilitators to fully activate gene expression (2023) · cites this paper as [81]
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“Peaks in ENCODE blacklisted regions (95) were removed using the intersect function in bedtools2 (96) v2.30.0.”
From Synergy between regulatory elements can render cohesin dispensable for distal enhancer function (2026) · cites this paper as [96]
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Metadata
- Authors
- Quinlan, A. R., & Hall, I. M.
- Affiliations
- University of Virginia (US)
- Corresponding author
- Quinlan, Aaron R.
- Hall, Ira M.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-01-28
- Volume
- 26
- Issue
- 6
- Pages
- 841-842
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC2832824
- OpenAlex
- W2102619694
- Cited by
- 27,437
- References
- 4
- Citations by year
- 2026: 2474 · 2025: 3385 · 2024: 3380 · 2023: 2862 · 2022: 2676 · 2021: 2957 · 2020: 2267 · 2019: 1731 · 2018: 1533 · 2017: 1185 · 2016: 932 · 2015: 743 · 2014: 616 · 2013: 387 · 2012: 212
- FWCI
- 88.15
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- Wellcome Trust
- National Institutes of Health (1dp2od006493-01)
- National Human Genome Research Institute (F32HG005197)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- bedtools, BAM alignment file, genome annotation, feature overlap, next-generation sequencing data
- MeSH terms
- Software, Genome, Internet, Genomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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