Bedtools

Introduction

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

Versions

• 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

Example job

Adjust slurm options based on job requirements (slurm cheat sheet):

#!/bin/bash
#SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
#SBATCH -N 1   # Number of nodes
#SBATCH -n 1   # Number of tasks per node
#SBATCH -c 4   # Number of CPU cores per task
#SBATCH --mem=8G       # Memory required per node
#SBATCH --job-name=bedtools    # Job name
#SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
#SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
#SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
#SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

module purge   ### Optional, but highly recommended.
module load bedtools/XXXX      ### Latest version is recommended.