Fastqc¶
FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.
Fastqc is available as a module on Apocrita.
Usage¶
To run the default installed version of Fastqc, simply load the fastqc
module:
$ module load fastqc
$ fastqc --help
FastQC - A high throughput sequence QC analysis tool
SYNOPSIS
fastqc seqfile1 seqfile2 .. seqfileN
fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam]
[-c contaminant file] seqfile1 .. seqfileN
Example job¶
Serial job¶
Here is an example job running on 1 core and 1GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
module load fastqc
fastqc raw_data.fastq.gz raw_data2.fastq.gz
Viewing the Fastqc results
To view the Fastqc results, you may open the fastqc_report.html file in
a web browser or the summary.txt file (located in the zipped output
archive) on the command line. For assistance copying files to your local
machine, please see the Moving Data page.