BEDTools statistics

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Citations per year

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Popular tool citations

chevron_left File indexation Known transcript quantification File format conversion File merging File filtering File sampling File comparison Tag count Motif comparison Depth of coverage File intersection File parsing-extraction File sorting chevron_right
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Associated diseases


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BEDTools specifications


Unique identifier OMICS_01159
Name BEDTools
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input format BED, BAM, VCF, GFF
Output format BED, BAM, VCF, GFF, BAI
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


  • coverageBed
  • IntersectBed
  • mergeBed
  • multiBamCov



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  • person_outline Aaron R. Quinlan <>

Publication for BEDTools

BEDTools in pipelines

PMCID: 5755908
PMID: 29304067
DOI: 10.1371/journal.pone.0190685

[…] previously []. briefly, transreads (reads spanning exon-exon junctions) were extracted using regtools 0.2.0 ( intron 5’ end base coverage was determined using bedtools 2.25.0 []. splicing efficiency was then calculated as the ratio of transreads (mrna) to intron-end reads (pre-mrna). enriched go categories were searched for using go term finder 0.83 […]

PMCID: 5760651
PMID: 29317678
DOI: 10.1038/s41467-017-02618-6

[…] orientation were collapsed to a single read before subsequent analysis. density profiles were created by extending each read to the average library fragment size and then computing density using the bedtools suite. enriched regions were discovered using macs 2.0 and scored against matched input libraries. genomic ‘blacklisted’ regions were filtered […]

PMCID: 5763571
PMID: 29321036
DOI: 10.1186/s12989-017-0239-8

[…] (fig. ). reads were then mapped to the rat genome (rn6) using the default parameters in bowtie2. to perform differential binding analysis on reads while distinguishing peaks, diffreps was used []. bedtools functions were used to delineate upstream promoter regions of genes (bedtools slop) and evaluate the promoter/gene overlay (bedtools intersect). genes were defined to include 1000 bases […]

PMCID: 5766238
PMID: 29293496
DOI: 10.1371/journal.pcbi.1005921

[…] from gencodev24. utr and cds coordinates were extracted from ensembl biomart. to assign only one 5utr sequence to one gene, we merged all annotated 5utrs associated with the gene of interest using bedtools merge [] and further concatenated all sequences. the same procedure was used for 3utrs and cdss. intron sequences are gencodev24 genes to which 5utr, 3utr and cds sequences described […]

PMCID: 5769542
PMID: 29337314
DOI: 10.1038/sdata.2017.203

[…] to the draft genomes were identified. based on the metagenomic reads recruited to the secondary contigs for each sample, the number of reads aligned to each marker in a sample was determined using bedtools (v2.17.0; multicov default parameters). a length-normalized estimate of relative abundance for each draft genome in each sample in a province was determined using the following equation: […]

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BEDTools in publications

PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] and h3k27ac peaks were called using the macs2 software package at false discovery rate (fdr) ≤ 1%. sicer was used to identify enriched domains for h3k27me3 and h3k9me3. for data visualization, bedtools in combination with in-house scripts were used to generate normalized tag density profile at a window size of 200 bp and step size of 20 bp. we also visualized the average profile around tss […]

PMCID: 5955993
PMID: 29769529
DOI: 10.1038/s41467-018-04426-y

[…] reads were aligned to the mouse reference genome mm8 and normalized by sequencing depth., h3k4me3 peak regions called for different methionine conditions and replicates were merged using the bedtools merge command in bedtools package to generate a combinational peak set for following annotation and computation of peak descriptors. peaks were assigned to genes with tss closest to center […]

PMCID: 5951945
PMID: 29760376
DOI: 10.1038/s41419-018-0604-z

[…] the gsm2424064_encff191ycr_fold_change_over_control_grch38.bigwig file was downloaded. we annotated those peaks by using r package “chipseeker”. subsequently, the gene region were intercepted with bedtools and exported to integrated genomics viewer software to map the peaks,., the function enrichments of differentially expressed genes were analysed with go classification and kyoto encyclopedia […]

PMCID: 5945709
PMID: 29748573
DOI: 10.1038/s41598-018-25895-7

[…] for reference mapping, we used the complete human genome data of homo sapiens (assembly grch38). read alignment was performed using bwa mem. the coverage in bins of 1 mbp size was determined using bedtools (see also fig. ). to assess the equality of the read-distribution we calculated the gini coefficient across 100 kb genomic bins using the r-package ineq (see fig. ). the gini coefficient […]

PMCID: 5941680
PMID: 29739336
DOI: 10.1186/s12864-018-4670-5

[…] and was therefore converted to 0-based coordinates to be consistent with the other three algorithms. we then annotated our catalog of circrna candidates using ucsc refseq annotations [] and bedtools []., the ratio of circular-to-linear rna isoforms was calculated using the approach described in []. for each circrna candidate, we used the number of back-spliced reads for circrna […]

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BEDTools institution(s)
Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine and Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA

BEDTools review

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Fabien Pichon

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Another indispensable tools suite to have, particularly if you work with .bed files, of course !
In comparison, however, Homer is better if you want to intersect further files because it gives more details, ideal to create a Venn diagram !
A big plus of bedtools : tools are very well documented, with schemes ! I like: "shuffle" to randomly relocate peaks, to test significance of a pathway enrichment for example !