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
bedtools2 module:
$ module load bedtools2
$ 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
#SBATCH --ntasks=1 # (or -n 1) Request 1 core
#SBATCH --mem-per-cpu=1G # Request 1GB RAM per core (1GB total)
#SBATCH --time=1:0:0 # (or -t 1:0:0) Request 1 hour runtime
module load bedtools2
# Report the base-pair overlap between the features in two BED files.
bedtools intersect -a reads.bed -b genes.bed