BEDTools: The Swiss-Army Tool for Genome Feature Analysis

Curr Protoc Bioinformatics. 2014 Sep 8;47:11.12.1-34. doi: 10.1002/0471250953.bi1112s47.


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.

Keywords: bioinformatics; genome analysis; genome features; genome intervals; genomics.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Computational Biology
  • Gene Expression
  • Genome*
  • High-Throughput Nucleotide Sequencing
  • Protein Binding
  • Sequence Analysis, DNA*
  • Software*
  • Transcription Factors / metabolism


  • Transcription Factors