Software: Bedtools
Description
Bedtools is an extensive suite of utilities for genome arithmetic and comparing genomic features in BED format.
Available Versions
| Unspecified: | 2.30.0 2.31.0 |
|---|
For more information, please check its website: https://biocontainers.pro/tools/bedtools and its home page on Github.
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
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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