Software: FastQC
Description
FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
Available Versions
| Unspecified: | 0.11.9 |
|---|
For more information, please check its website: https://biocontainers.pro/tools/fastqc and its home page: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
Commands
- fastqc
Module
You can load the modules by:
module load biocontainers
module load fastqc
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
To run Fastqc on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=fastqc
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers fastqc
fastqc -o fastqc_out -t 4 FASTQ1 FASTQ2