Fastqc

Notitle

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 latest 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 jobs

Serial job

Here is an example job running on 1 core and 1GB memory:

#!/bin/sh
#$ -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.

References