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Circexplorer on Biowulf & Helix

Description

CIRCexplorer is a combined strategy to identify junction reads from back spliced exons and intron lariats.

There may be multiple versions available on our systems. An easy way of selecting the version is to use modules. To see the modules available, type

module avail circexplorer 

To select a module use

module load circexplorer/[version]

where [version] is the version of choice.

Environment variables set
Documentation

https://github.com/YangLab/CIRCexplorer

Circexplorer job on Biowulf

Allocate an interactive session with sinteractive and use as described below

biowulf$ sinteractive --mem=5g
salloc.exe: Pending job allocation 38978697
[...snip...]
salloc.exe: Nodes cn2273 are ready for job
node$ module load circexplorer
[+] Loading circexplorer
node$ CIRCexplorer.py -f accepted_hits.bam -g hg19.fa -r ref.txt
[...snip...]
node$ exit
biowulf$

 

Batch job on Biowulf

Create a batch script similar to the following example:

#! /bin/bash
# this file is circexplorer.batch

module load circexplorer || exit 1
cd /data/$USER
CIRCexplorer.py -f accepted_hits.bam -g hg19.fa -r ref.txt

Submit to the queue with sbatch:

biowulf$ sbatch circexplorer.batch

 

Swarm of Jobs on Biowulf

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

# this file is called script.swarm
cd dir1;circexplorer command 1;circexplorer command 2
cd dir2;circexplorer command 1;circexplorer command 2
cd dir3;circexplorer command 1;circexplorer command 2
[...]

Submit this job using the swarm command.

swarm -f script.swarm --module circexplorer

For more information regarding swarm: https://hpc.nih.gov/apps/swarm.html#usage