bedtools.rst

Bedtools

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

For more information, please check its website: https://biocontainers.pro/tools/bedtools and its home page on Github.

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

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 -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
ml biocontainers bedtools

bedtools intersect -a a.bed -b b.bed
bedtools annotate -i variants.bed -files genes.bed conserve.bed known_var.bed