22    ◾    Bioinformatics

The zipped file contains the images and the text files that will be displayed on the HTML

when it is opened on an Internet browser. We can display the HTML files from the Linux

­terminal using Firefox. If Firefox is not installed, use “sudo apt-get install firefox” to

install it. If you are using Putty to access a remote computer, you may need to enable “X11

Forwarding”.

Use the following syntax to display the QC reports:

firefox HTMLfile1 HTMLfile2 .. HTMLfileN

Alternatively, you can use a bash script as follows:

cd qc

htmlfiles=$(ls *.html)

firefox $htmlfiles

cd ..

The Firefox Internet browser will display the QC FastQC reports of all FASTQ files, each

on a separate tab as shown in Figure 1.11. Click a tab to move from a report to another.

A QC FastQC report includes a summary, basic statistics, and the quality control met-

rics that we will discuss in some detail. Summary, on the left-hand side, provides a quick

visual report to the different QC metrics available in the report and allows us to identify

any existing problem. With each metric title, Summary displays a sign indicating whether

there is any potential quality problem; the green color indicates a normal metric, orange

indicates a slightly abnormal metric, and red indicates a quality problem associated with

the metric. A metric with an orange warning requires an attention and correction if it is

possible and a metric with a red warning indicates that there is a clear fault in the sequence

data and it is recommended to fix it before proceeding to the analysis step. Summary also

FIGURE 1.11  QC FastQC reports.