Attention

WARNING: From 8am on 30th June until 5pm on 4th July 2025, there will be no access to the Stanage HPC cluster.

We will try to minimise this downtime and it is possible that Stanage will return to service before 4th July. We will notify you by email when Stanage is back online and available for job submission.

Bedtools

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks.

Interactive usage

After connecting to Stanage (see Establishing a SSH connection), start an interactive session with the following command:

srun --pty bash -i

The latest version of bedtools (currently version 2.31.0) is made available with the command:

module load BEDTools/2.31.0-GCC-12.3.0

After this any of the bedtools commands can be run from the prompt.

Installation notes

Bed tools was installed using EasyBuild/4.9.4, build details can be found in $EBROOTBEDTOOLS/easybuild with the module loaded.