pybedtools pipeline

pybedtools specifications


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 pipeline

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 [52], gffutils v0.8, and bedtools v2.16.2 [53]., feature classes [tsss (1 bp transcript start position), cdss, introns, 5′utrs, and 3′utrs] were extracted from all annotated isoforms […]

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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