Volume 47, Issue 1 p. 11.12.1-11.12.34

BEDTools: The Swiss-Army Tool for Genome Feature Analysis

Aaron R. Quinlan

Aaron R. Quinlan

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

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First published: 08 September 2014
Citations: 1,159


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. Curr. Protoc. Bioinform. 47:11.12.1-11.12.34. © 2014 by John Wiley & Sons, Inc.