title: BEDTools: The Swiss-Army Tool for Genome Feature Analysis.
abstract: Technological advances have enabled the use of DNA sequencing as a flexible tool to characterize genetic variation and to measure the activity of diverse cellular phenomena such as gene isoform expression and transcription factor binding. Extracting biological insight from the experiments enabled by these advances demands the analysis of large, multi-dimensional datasets. This unit describes the use of the BEDTools toolkit for the exploration of high-throughput genomics datasets. Several protocols are presented for common genomic analyses, demonstrating how simple BEDTools operations may be combined to create bespoke pipelines addressing complex questions.
authors.affiliation: Department of Public Health Sciences, Center for Public Health Genomics, Department of Biochemistry and Molecular Genetics, and Department of Computer Science. University of Virginia, Charlottesville, Virginia.
authors.forename: Aaron R
authors.initials: AR
authors.lastname: Quinlan
mesh_terms: D019295:Computational Biology; D015870:Gene Expression; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D011485:Protein Binding; D017422:Sequence Analysis, DNA; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors
keywords: bioinformatics; genome analysis; genome features; genome intervals; genomics