CIRCexplorer2 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 circexplorer2 

To select a module use

module load circexplorer2/[version]

where [version] is the version of choice.

• $PATH
• database files in /fdb/circexplorers2

https://github.com/YangLab/CIRCexplorer

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 circexplorer2
[+] Loading circexplorer2
node$ CIRCexplorer2.py -f accepted_hits.bam -g hg19.fa -r ref.txt
[...snip...]
node$ exit
biowulf$

Create a batch script similar to the following example:

#! /bin/bash
# this file is circexplorer2.batch

module load circexplorer2 || exit 1
cd /data/$USER
CIRCexplorer2.py -f accepted_hits.bam -g hg19.fa -r ref.txt

Submit to the queue with sbatch:

biowulf$ sbatch circexplorer2.batch

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

# this file is called script.swarm
cd dir1;circexplorer2 command 1;circexplorer2 command 2
cd dir2;circexplorer2 command 1;circexplorer2 command 2
cd dir3;circexplorer2 command 1;circexplorer2 command 2
[...]

Submit this job using the swarm command.

swarm -f script.swarm --module circexplorer2

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