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.

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