miRDeep2

Overview

miRDeep2 is a program for identification of novel and known miRNAs in deep sequencing data. Furthermore, it can be used for miRNA expression profiling across samples.

Versions 0.1.1 and 0.1.3 are installed on the CSF.

Restrictions on use

There are no restrictions on accessing the software on the CSF. It is release under the GNU GPL v3 license and all usage must adhere to that license.

Set up procedure

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.

Load one of the following modulefiles:

module load apps/binapps/mirdeep2/0.1.3       # Note the different modulefile names
module load apps/mirdeep2/0.1.1

Running the application

Please do not run miRDeep2 on the login node. Jobs should be submitted to the compute nodes via batch. There are a number of perl scripts provided by miRDeep2 – please see the miRDeep2 script reference for how to run these tools.

Serial batch job submission

Create a batch submission script (which will load the modulefile in the jobscript), for example:

#!/bin/bash --login
#$ -cwd             # Job will run from the current directory
                    # NO -V line - we load modulefiles in the jobscript

module load apps/binapps/mirdeep2/0.1.3

miRDeep2.pl fasta input files

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Further info

• miRDeep2 website

Updates

None.