FastQC

Overview

FastQC is a quality control tool for high throughput sequence data. The application is written in Java and can be used in batch or interactively (via the qrsh command).

Version 0.11.3 is installed on the CSF.

Restrictions on use

There are no restrictions on using this software on the CSF. The application is released under the GPL v3 license.

Set up procedure

To access the software you must first load the modulefile:

module load apps/binapps/fastqc/0.11.3

Running the application

Please do not run FastQC on the login node. Jobs should be submitted to the compute nodes via batch or run interactively via the qrsh command.

Serial batch job submission

Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd             # Job will run from the current directory
#$ -V               # Job will inherit current environment settings

# Specify a list of files to process
fastqc inputfile1.txt inputfile2.txt

# Note: If wishing to process compressed .fastq.gz file, use the following:
zcat *fastq.gz | fastqc stdin

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Interactive use of the GUI

FastQC can be run interactively but this must not be run on the login node. Instead you must schedule an interactive session on a compute node. Use the following commands (after loading the modulefile):

qrsh -l inter -l short -V fastqc

This will only run when a free core is available on one of the interactive nodes. If no free resources are available you will be asked to try again later.

Further info

• Brief notes on command-line flags are available on the CSF using:

  less $FASTQC_HOME/Install.txt
  
  FastQC website
  

Updates

None.