Bedtools¶
The Bedtools suite is a collection of tools for a wide-range of genomics analysis tasks.
Bedtools is available as a module on Apocrita.
Usage¶
To run the default installed version of Bedtools, simply load the
bedtools module:
$ module load bedtools
$ bedtools -h
Usage: bedtools <subcommand> [options]
For full usage documentation, run bedtools -h.
Example job¶
Serial job¶
Here is an example job running on 1 core and 1GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
module load bedtools
# Report the base-pair overlap between the features in two BED files.
bedtools intersect -a reads.bed -b genes.bed