Bedops

Introduction

Bedops is a software package for manipulating and analyzing genomic interval data.

For more information, please check its website: https://biocontainers.pro/tools/bedops and its home page: https://bedops.readthedocs.io/en/latest/.

Versions

  • 2.4.39

Commands

  • bam2bed

  • bam2bed-float128

  • bam2bed_gnuParallel

  • bam2bed_gnuParallel-float128

  • bam2bed_gnuParallel-megarow

  • bam2bed_gnuParallel-typical

  • bam2bed-megarow

  • bam2bed_sge

  • bam2bed_sge-float128

  • bam2bed_sge-megarow

  • bam2bed_sge-typical

  • bam2bed_slurm

  • bam2bed_slurm-float128

  • bam2bed_slurm-megarow

  • bam2bed_slurm-typical

  • bam2bed-typical

  • bam2starch

  • bam2starch-float128

  • bam2starch_gnuParallel

  • bam2starch_gnuParallel-float128

  • bam2starch_gnuParallel-megarow

  • bam2starch_gnuParallel-typical

  • bam2starch-megarow

  • bam2starch_sge

  • bam2starch_sge-float128

  • bam2starch_sge-megarow

  • bam2starch_sge-typical

  • bam2starch_slurm

  • bam2starch_slurm-float128

  • bam2starch_slurm-megarow

  • bam2starch_slurm-typical

  • bam2starch-typical

  • bedextract

  • bedextract-float128

  • bedextract-megarow

  • bedextract-typical

  • bedmap

  • bedmap-float128

  • bedmap-megarow

  • bedmap-typical

  • bedops

  • bedops-float128

  • bedops-megarow

  • bedops-typical

  • closest-features

  • closest-features-float128

  • closest-features-megarow

  • closest-features-typical

  • convert2bed

  • convert2bed-float128

  • convert2bed-megarow

  • convert2bed-typical

  • gff2bed

  • gff2bed-float128

  • gff2bed-megarow

  • gff2bed-typical

  • gff2starch

  • gff2starch-float128

  • gff2starch-megarow

  • gff2starch-typical

  • gtf2bed

  • gtf2bed-float128

  • gtf2bed-megarow

  • gtf2bed-typical

  • gtf2starch

  • gtf2starch-float128

  • gtf2starch-megarow

  • gtf2starch-typical

  • gvf2bed

  • gvf2bed-float128

  • gvf2bed-megarow

  • gvf2bed-typical

  • gvf2starch

  • gvf2starch-float128

  • gvf2starch-megarow

  • gvf2starch-typical

  • psl2bed

  • psl2bed-float128

  • psl2bed-megarow

  • psl2bed-typical

  • psl2starch

  • psl2starch-float128

  • psl2starch-megarow

  • psl2starch-typical

  • rmsk2bed

  • rmsk2bed-float128

  • rmsk2bed-megarow

  • rmsk2bed-typical

  • rmsk2starch

  • rmsk2starch-float128

  • rmsk2starch-megarow

  • rmsk2starch-typical

  • sam2bed

  • sam2bed-float128

  • sam2bed-megarow

  • sam2bed-typical

  • sam2starch

  • sam2starch-float128

  • sam2starch-megarow

  • sam2starch-typical

  • sort-bed

  • sort-bed-float128

  • sort-bed-megarow

  • sort-bed-typical

  • starch

  • starchcat

  • starchcat-float128

  • starchcat-megarow

  • starchcat-typical

  • starchcluster_gnuParallel

  • starchcluster_gnuParallel-float128

  • starchcluster_gnuParallel-megarow

  • starchcluster_gnuParallel-typical

  • starchcluster_sge

  • starchcluster_sge-float128

  • starchcluster_sge-megarow

  • starchcluster_sge-typical

  • starchcluster_slurm

  • starchcluster_slurm-float128

  • starchcluster_slurm-megarow

  • starchcluster_slurm-typical

  • starch-diff

  • starch-diff-float128

  • starch-diff-megarow

  • starch-diff-typical

  • starch-float128

  • starch-megarow

  • starchstrip

  • starchstrip-float128

  • starchstrip-megarow

  • starchstrip-typical

  • starch-typical

  • switch-BEDOPS-binary-type

  • unstarch

  • unstarch-float128

  • unstarch-megarow

  • unstarch-typical

  • update-sort-bed-migrate-candidates

  • update-sort-bed-migrate-candidates-float128

  • update-sort-bed-migrate-candidates-megarow

  • update-sort-bed-migrate-candidates-typical

  • update-sort-bed-slurm

  • update-sort-bed-slurm-float128

  • update-sort-bed-slurm-megarow

  • update-sort-bed-slurm-typical

  • update-sort-bed-starch-slurm

  • update-sort-bed-starch-slurm-float128

  • update-sort-bed-starch-slurm-megarow

  • update-sort-bed-starch-slurm-typical

  • vcf2bed

  • vcf2bed-float128

  • vcf2bed-megarow

  • vcf2bed-typical

  • vcf2starch

  • vcf2starch-float128

  • vcf2starch-megarow

  • vcf2starch-typical

  • wig2bed

  • wig2bed-float128

  • wig2bed-megarow

  • wig2bed-typical

  • wig2starch

  • wig2starch-float128

  • wig2starch-megarow

  • wig2starch-typical

Module

You can load the modules by:

module load biocontainers
module load bedops

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 Bedops on our clusters:

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

module --force purge
ml biocontainers bedops

bedops -m 001.merge.001.test > 001.merge.001.observed
bedops -c 001.merge.001.test > 001.complement.001.observed
bedops -i 001.intersection.001a.test 001.intersection.001b.test > 001.intersection.001.observed