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
#SBATCH -n 1               # (or --ntasks=1) Request 1 core
#SBATCH --mem-per-cpu=1G   # Request 1GB RAM per core
#SBATCH -t 1:0:0           # Request 1 hour runtime

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.

Fastqc¶

Usage¶

Example job¶

Serial job¶

References¶