bedtools
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'bedtools' Versions
- 2.30.0
Link to section 'Commands' of 'bedtools' 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
Link to section 'Module' of 'bedtools' Module
You can load the modules by:
module load biocontainers
module load bedtools
Link to section 'Example job' of 'bedtools' Example job
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