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
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