bedtools

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. While each individual tool is designed to do a relatively simple task, quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

Availability and Restrictions

The following versions of bedtools are available on OSC clusters:

Version Oakley Owens
2.25.0 X* X*
*: Current default version

You can use  module spider bedtools  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

bedtools is available to all OSC users without restriction.

Usage on Oakley

Set-up

To configure your environment for use of bedtools, run the following command:   module load bedtools . The default version will be loaded. To select a particular bedtools version, use   module load bedtools/version  . For example, use  module load bedtools/2.25.0   to load bedtools 2.25.0.

Usage on Owens

Set-up

To configure your environment for use of bedtools, run the following command:   module load bedtools . The default version will be loaded. To select a particular bedtools version, use   module load bedtools/version  . For example, use  module load bedtools/2.25.0   to load bedtools 2.25.0.

Further Reading

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