Bedtools

Introduction

Bedtools is an extensive suite of utilities for genome arithmetic and comparing genomic features in BED format.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/bedtools
Home page: https://github.com/arq5x/bedtools2

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

2.30.0, 2.31.0

BELL

2.30.0, 2.31.0

GAUTSCHI

2.30.0, 2.31.0

NEGISHI

2.30.0, 2.31.0

SCHOLAR

2.30.0, 2.31.0

Commands

  • annotateBed

  • bamToBed

  • bamToFastq

  • bed12ToBed6

  • bedpeToBam

  • bedToBam

  • bedToIgv

  • bedtools

  • closestBed

  • clusterBed

  • complementBed

  • coverageBed

  • expandCols

  • fastaFromBed

  • flankBed

  • genomeCoverageBed

  • getOverlap

  • groupBy

  • intersectBed

  • linksBed

  • mapBed

  • maskFastaFromBed

  • mergeBed

  • multiBamCov

  • multiIntersectBed

  • nucBed

  • pairToBed

  • pairToPair

  • randomBed

  • shiftBed

  • shuffleBed

  • slopBed

  • sortBed

  • subtractBed

  • tagBam

  • unionBedGraphs

  • windowBed

  • windowMaker

Module

You can load the modules by:

module load biocontainers
module load bedtools

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run bedtools on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bedtools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers bedtools

# Your bedtools workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bedtools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers bedtools

# Your bedtools workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bedtools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers bedtools

# Your bedtools workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bedtools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers bedtools

# Your bedtools workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bedtools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers bedtools

# Your bedtools workflow...