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BEDOPS specifications


Unique identifier OMICS_00949
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input data BEDOPS supports a relaxed variation of the BED specification, to which several popular formats, including WIG, SAM/BAM, VCF and GFF, readily convert. Thus, data currently stored in any of these formats can be transformed and analyzed using features offered by BEDOPS.
Input format BED, WIG, SAM, BAM, VCF, GFF,
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.4.15
Stability Stable
Maintained Yes




No version available


Publication for BEDOPS

BEDOPS citations


Distinctive epigenomes characterize glioma stem cells and their response to differentiation cues

Genome Biol
PMCID: 5872397
PMID: 29587824
DOI: 10.1186/s13059-018-1420-6

[…] Differential enrichment was identified using SICER-diff at FDR < 0.01. Unique and common differentially enriched peaks across all glioma stem-cell lines vs neural stem-cell lines were identified with BEDOPS v2.4.20. The R package “ChIPseeker” was used to annotate ChIP peaks with general genomic features and compare feature distribution across different subsets of peaks. Tag density plots of transc […]


Global analysis of primary mesenchyme cell cis regulatory modules by chromatin accessibility profiling

BMC Genomics
PMCID: 5859501
PMID: 29558892
DOI: 10.1186/s12864-018-4542-z

[…] -seq data by first identifying all replicate peaks that overlapped by at least 75% non-reciprocally and then merging all such peaks across samples separately for the DNase-seq or ATAC- seq data using Bedops (v2.4.2) []. The 75% overlap criterion was enforced non-reciprocally in order to account for differences in peak sizes across replicates. For example, if a 75% or greater overlap was enforced r […]


Circular DNA elements of chromosomal origin are common in healthy human somatic tissue

Nat Commun
PMCID: 5852086
PMID: 29540679
DOI: 10.1038/s41467-018-03369-8

[…] All intersection operations between eccDNA intervals were set for a reciprocal overlap of at least 90%, using Bedops. Intersection profiles and merged tracks were plotted into a genome map using a modified source code of w4Cseq. […]


Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regions

Nucleic Acids Res
PMCID: 5829566
PMID: 29216379
DOI: 10.1093/nar/gkx1214

[…] rongest changes in response to hypoxia were selected by using log2 fold change cutoff 1 for H3K27ac and cutoff 4 for H3K4me1 data. To assess CTCF binding in MCF-7 cells (), closest features tool from BEDOPS software () was used to select CTCF peaks closest to hypoxia-inducible factor 1 alpha (HIF1α) peaks (found in both HUVEC and MCF-7 datasets ()) or TSS of hypoxia-regulated genes that were share […]


Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease

Sci Rep
PMCID: 5686184
PMID: 29138457
DOI: 10.1038/s41598-017-15822-7

[…] aks of H3K4me1 and H3K27ac, and the P-values of H3K4me1 and H3K27ac were set to 10−6 and 10−9, respectively. The control for peak calling was obtained by merging all the replicates of the input using BEDOPS with the parameter “-everything”. For peaks of H3K4me1 and H3K27ac with two or more replicates, we chose only those that appeared in over 70% of the replicates and merged all the peaks from mul […]


A Paradoxical Tumor Suppressor Role for the Rac1 Exchange Factor Vav1 in T Cell Acute Lymphoblastic Leukemia

Cancer Cell
PMCID: 5691892
PMID: 29136506
DOI: 10.1016/j.ccell.2017.10.004

[…] value ≤ 10−5. hg18 coordinates were converted to the hg19 assembly using the LiftOver utility of the UCSC Genome Browser Tools. Wig files were converted to bed format using the wig2bed utility of the BEDOPS Suite. Visualization of data was performed in R using the Gviz package. The accession codes for the datasets used are GSE62144 (for TLX1) and GSE51800 (for Ets1 and Runx1). In the case of ChIP- […]


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BEDOPS institution(s)
Department of Genome Sciences, University of Washington, Seattle, WA, DC, USA; Department of Medicine, University of Washington, Seattle, WA, DC, USA
BEDOPS funding source(s)
National Institutes of Health Grants (1U54HG004592 and 5U01ES017156)

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