Updated 2020-04-07

Run FastQC Interactively on the Cluster

Overview

  • Running FastQC on the cluster follows the same general steps as any interacive job. These steps are:
    • Set up VNC Session
    • Load fastqc module. Use module avail fastqc to see what versions of fastqc are available
    • Run FastQC with the command fastqc

Set up VNC Session

  • Please see the VNC guide for instructions on how to set up the Interactive VNC session

Load FastQC

  • Open a terminal in the vnc window by clicking top left Applications > System Tools > scroll down to terminal
  • All commands here on will be typed in terminal in VNC
  • On the cluster, fastqc/0.10.1 and fastqc/0.11.2 are available
  • module load fastqc/0.11.2 will load fastqc. Replace the number at the end with the version number you want to load

Run FastQC

  • Run with the command fastqc * Screenshot