BEDOPS

BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable set, statistical and multi-processing operations on genomic intervals in BED format. It includes tools such as bedops (set operations), bedmap (mapping and statistics), sort-bed (sorting) and closest-features.

BEDOPS

License

Free to use and open source under GNU GPLv2.

Available

Roihu: 2.4.42, via the bio-apps module.

Usage

BEDOPS is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the BEDOPS module:

module load bio-apps/v202603
module load bedops/2.4.42

Most BEDOPS operations require sorted BED input, which you can produce with sort-bed:

sort-bed unsorted.bed > sorted.bed

You can then perform set operations, for example finding the intersection of two BED files:

bedops --intersect a.sorted.bed b.sorted.bed > intersection.bed

Example batch script

#!/bin/bash
#SBATCH --job-name=bedops
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=4G

module load bio-apps/v202603
module load bedops/2.4.42

bedops --intersect a.sorted.bed b.sorted.bed > intersection.bed

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk