Bedops

Introduction

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

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

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=bedops      # 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 bedops/XXXX        ### Latest version is recommended.