pybedtools protocols

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pybedtools specifications

Information


Unique identifier OMICS_09508
Name pybedtools
Software type Package/Module
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 Python
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.6.9
Stability Stable
Maintained Yes

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  • person_outline Aaron R. Quinlan <>

Publication for pybedtools

pybedtools in pipelines

 (4)
2018
PMCID: 5861125
PMID: 29559621
DOI: 10.1038/s41467-018-03575-4

[…] were used. motifs were generated based on the 5% highest-scoring peaks among the 10,000 bound training instances., venn diagrams comparing uvclap, par-clip, and eclip peaks were created using pybedtools (version 0.7.9)., flag-hrp (sigma-aldrich, a8592) used at 1:2000 dilution in fig. , supplementary fig. , and supplementary fig. . sam68 (khrdbs1) polyclonal antibody (sigma-aldrich, s9575) […]

2016
PMCID: 4844672
PMID: 27097556
DOI: 10.1038/ncomms11222

[…] following the manufacturer's instructions., bioinformatics analyses were performed using the shore suite (version 0.9.3) (ref. ) and scripts in python (version 2.7.3) using biopython (version 1.60), pybedtools (version 0.6.4) and matplotlib (version 1.2.0) modules. all statistical analyses were managed using r (version 3.0.2) and figures were generated using the ggplot2 module (version 1.0.0). […]

2014
PMCID: 4183418
PMID: 25275310
DOI: 10.1371/journal.pgen.1004648

[…] for the analysis of the distribution of pxr chip-seq peaks following rifampin treatment, we used knowngene from the ucsc genome browser to define the transcription start site (tss) as the center and pybedtools for the calculations followed by matplotlib (http://matplotlib.org) to plot., selected promoters were obtained from the lightswitch promoter collection (switchgear genomics) and sequence […]

2012
PMCID: 3510032
PMID: 23209434
DOI: 10.1371/journal.pgen.1003069

[…] were merged. sequence data are deposited in the gene expression omnibus under accession number gse40797., intersections, classification, and randomizations in the below analyses were performed with pybedtools v0.6 , gffutils v0.8, and bedtools v2.16.2 ., feature classes [tsss (1 bp transcript start position), cdss, introns, 5′utrs, and 3′utrs] were extracted from all annotated isoforms […]


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pybedtools in publications

 (31)
PMCID: 5916898
PMID: 29695722
DOI: 10.1038/s41467-018-04084-0

[…] using the ucsc genome browser liftover tool. all g4 peaks from the plus and minus strand with overlapping coordinates were combined using bedtools. we used automated permutation-based testing with pybedtools to look for significant correlation between chip-seq peaks and g4-seq peaks. we randomized chip-seq peaks 1000 times over the genome and each time measured the peak intersection […]

PMCID: 5861125
PMID: 29559621
DOI: 10.1038/s41467-018-03575-4

[…] were used. motifs were generated based on the 5% highest-scoring peaks among the 10,000 bound training instances., venn diagrams comparing uvclap, par-clip, and eclip peaks were created using pybedtools (version 0.7.9)., flag-hrp (sigma-aldrich, a8592) used at 1:2000 dilution in fig. , supplementary fig. , and supplementary fig. . sam68 (khrdbs1) polyclonal antibody (sigma-aldrich, s9575) […]

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

[…] the split-read mapped to multiple positions in the genome., the likelihood of detected overlaps between rna split-transcripts and eccdna coordinates was assessed by monte carlo simulations, using pybedtools. eccdna coordinates and rna split-transcript intervals were randomized on the human genome 1,000 times and an empirical p-value was computed based on the number of random intersections […]

PMCID: 5864089
PMID: 29529026
DOI: 10.1371/journal.pgen.1007276

[…] we therefore selected final peaks for pol ii as those peaks in the pooled peak-calling run that were also found in at least one of the individual replicates. specifically, using bedtools v2.25.0 and pybedtools v0.7.9 [,] we used "pooled.intersect([replicates], u = true).sort().merge()" where "pooled" points to the pooled peak calls and "[replicates]" is the list of individual peak calls […]

PMCID: 5821087
PMID: 29463659
DOI: 10.1128/mBio.02275-17

[…] information., we also performed a detailed coverage sequence depth analysis on 1-kb sliding windows by using 200-base intervals. we generated corresponding bed files with the window function in pybedtools for primary contigs and haplotigs. in addition, we generated corresponding sliding window bed files for primary contig regions that aligned with haplotig regions and for regions […]


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pybedtools institution(s)
Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA; Department of Medicine, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO, USA; Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
pybedtools funding source(s)
Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases

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