Bedtools¶

The Bedtools suite is a collection of tools for a wide-range of genomics analysis tasks.

Installation¶

You can check the installation guide here.

Usage¶

To run the default installed version of Bedtools, simply load the bedtools module:

$ 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

# Report the base-pair overlap between the features in two BED files.
bedtools intersect -a reads.bed -b genes.bed

Links¶

Reference¶

Hania Kranas