FastQC
FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.[1][2]
Installed Versions
FastQC 0.11.9 is installed on Picotte. Use the modulefile:
fastqc/0.11.9
Using
Remote Display
FastQC has a Graphical User Interface (GUI). To run it, appropriate X11 display software must be installed on your PC (Windows or macOS; Linux has it installed by default). See:
Then, FastQC can be run interactively on a compute node. See: Running GUI Applications on Compute Nodes
Multithreading
FastQC is multithreaded. You can request up to 48 CPU cores (1 core per thread) but there is no guarantee that performance scales linearly with number of threads.
Specify number of threads by using the SLURM_NPROCS environment
variable[3] rather than a literal integer. For example, requesting 16
(up to 48 is possible):
[juser@picotte001 ~]$ srun --x11 --nodes=1 --ntasks=1 --cpus-per-task=16 --mem=60G --pty /bin/bash
[juser@node042 ~]$ module load fastqc
[juser@node042 ~]$ fastqc --threads $SLURM_NPROCS
N.B. the window color may be reversed, i.e. black background.
Image:FastQC application window.png
References
[1] FastQC web page