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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

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.

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

More information