Quick Links Documentation Notes Interactive job Batch job Swarm of jobs

Bedops is a software package for manipulating and analyzing genomic interval data. It contains tools to

• perform boolean and set operations on genome intervals
• carry out statistical calculations on genome intervals
• sort bed files consistently (important for a lot of operations)
• compress genomic data using it's own starch format
• conversions of various formats (bam, gff/gtf, wig, vcf) to bed and starch

Operations can be parallelized efficiently by chromosome.

Each tool is designed to use unix input and output streams for building efficient pipelines.

References:

Shane Neph, et al. BEDOPS: high-performance genomic feature operations Bioinformatics 2012, 28:1919-1920. Pubmed |  PMC |  Journal

• GitHub
• Manual
• Overview
• Examples

• Module Name: bedops (see the modules page for more information)

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ convert2bed --input=bam --output=starch --starch-note "wt/H3ac/a13" < bam_inputfile > starch/a13.starch
[user@cn3144 ~]$ unstarch --note starch/a13.starch wt/H3ac/a13
[user@cn3144 ~]$ unstarch --elements starch/a13.starch
[user@cn3144 ~]$ unstarch --bases-uniq starch/a13.starch

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. bedops.sh). For example:

#!/bin/bash
set -e
module load bedops
sort-bed in.bed > out.bed

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] bedops.sh

Create a swarmfile (e.g. bedops.swarm). For example:

cd dir1; sort-bed in.bed > out.bed
cd dir2; sort-bed in.bed > out.bed
cd dir3; sort-bed in.bed > out.bed
cd dir4; sort-bed in.bed > out.bed

Submit this job using the swarm command.

swarm -f bedops.swarm [-g #] --module bedops

where

-g #	Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module	Loads the module for each subjob in the swarm