Sequencing and Raw Sequence Data Quality Control    ◾    19

unzip fastqc_v0.11.9.zip

A directory named “FastQC” containing the program files will be created.

Change to that directory with:

cd FastQC

This directory contains several files but we will focus only on “fastqc” file, which is the pro-

gram command that we will use and “Configuration” directory which contains three files

“adapter_list.txt”, “contaminant_list.txt”, and “limits.txt”, which can be used to configure

the QC report.

Use the Linux command “chmod” to make “fastqc” file executable:

chmod 755 fastqc

You may need to add the program to the Linux path so that you can use it from any direc-

tory. To do that, open the file “~/.bashrc” with any text editor and add the program path to

the end of the file, save the file and exit.

export PATH=”/home/mypath/FastQC”:$PATH

You may need to replace “/home/mypath” in the above statement with the path of your

downloaded FastQC.

You need to restart the terminal or you can use “source” command to make that change

active.

source ~/.bashrc

Finally, test the FastQC from any directory with the following:

fasqc -h

If the path was set correctly, you will see the program help screen.

On Linux, the FastQC program can also be installed simply by running “sudo apt-get

install fastqc”. Once it has been installed, you do not need any further configuration as we

did above. Although any one of the two installation methods works, in the first method,

you will know where you download the program and you can reach the “Configuration”

directory easily to make changes to any of the three configuration files stored there.

The FastQC program can be run in one of two modes: either as (i) an interactive graphi-

cal user interface (GUI) in which we can load FASTQ files and view their results or (ii) as a

non-interactive mode on a command line where we can specify the FASTQ files and then it

will generate an HTML report for each file. However, if we run it non-interactively, to display

the report, we will need to open the HTML files on an Internet browser. The command-line

mode allows FastQC to be run as part of an analysis pipeline. FastQC uses a FASTQ file as