Pittsburgh Supercomputing Center 

Advancing the state-of-the-art in high-performance computing,
communications and data analytics.

BEDTools

 

BEDTools is a collection of utilities for comparing, summarizing, and intersecting genomic features in the UCSC Genome Browser BED format. BEDTools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.

Documentation:

Usage

  • Bridges

  • Greenfield

  • BioU

 

To see what other modules are needed, what commands are available and how to get additional help type

module help bedtools

 

To see what versions of BEDtools are available type

module avail bedtools

 

To use BEDtools, include a command like this in your batch script to load the BEDTools module:

module load bedtools

Be sure you also load any other modules needed, as listed by the module help bedtools command.

 

To see what other modules are needed, what commands are available and how to get additional help type

module help bedtools

 

To see what versions of BEDtools are available type

module avail bedtools

 

To use BEDtools, include a command like this in your batch script to load the BEDTools module:

module load bedtools

Be sure you also load any other modules needed, as listed by the module help bedtools command.

 

The BEDTools programs are available through the Galaxy instance on biou.

To make the BEDTools programs available through the command line, csh users should enter the following command:

source /packages/bin/SETUP_BIO_SOFTWARE

To make the BEDTools programs available through the command line, bash users should enter the following command:

source /packages/bin/SETUP_BIO_SOFTWARE

 

 

 

See more help on BEDTools