STAR

Overview

STAR is a program to perform Spliced Transcripts Alignment to a Reference

Versions 2.4.2a, 2.5.1a, 2.5.3a and 2.7.2b are installed on the CSF.

Restrictions on use

There are no restrictions on accessing the software on the CSF. It is released under the MIT 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:

# Please note the different modulefile paths between versions!

# Load one of the following modulefiles
module load apps/binapps/star/2.7.2b             # Also provides STARlong for long reads

module load apps/intel-18.0/star/2.7.2b          # Intel compiler version (might be faster
                                                 # than the binapps pre-compiled version)
                                                 # Also provides STARlong for long reads

module load apps/star/2.5.3a                     # ONLY provides STAR

# These older versions and 'long reads' versions require you to first load:
module load apps/bioinf

# Then you can load one of:
module load apps/star/2.5.1a           # ONLY provides STAR
module load apps/star/2.4.2a           # ONLY provides STAR

module load apps/star_long/2.5.3a      # ONLY provides STARlong
module load apps/star_long/2.4.2a      # ONLY provides STARlong

Running the application

Please do not run STAR on the login node. Jobs should be submitted to the compute nodes via batch.

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

# Load the modulefile for the version you require
module load apps/binapps/star/2.7.2b

# $NSLOTS will be set to the number of cores requested (or 1 for a serial job)
STAR --runThreadN $NSLOTS --genomeDir REFERENCE --readFilesIn R1.fq R2.fq
  #
  # Use STARlong for 'long reads' version

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Parallel batch job submission