Fastqc Linux Install and Usage (Commandline & GUI) | Hello World Bioinformatics

This tutorial shows you how to install and run fastqc on a linux environment. fastqc is a bioinformatics tool used for quality control

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Materials
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link to example data

How to install java


Chapters
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00:03 Introduction
00:51 PC requirement
01:20 How to install java
01:41 Go to fastqc download page
02:18 Fetch the download link
02:30 Open the terminal
02:35 Move to the home directory
02:40 Usee wget to download the binaries
03:16 Unzip the file
03:56 Add execution rights to the fastqc executable
04:22 Test fastqc
04:51 Open the fastqc graphical interface
06:56 Move the fastqc directory to the apps directory
08:09 Move to the fastqc directory
08:27 Get the path of fastqc executable
09:10 Move to the home directory
09:17 Make a backup of the .bashrc file
09:48 Open .bashrc file
10:05 Add the path of fastqc to the system PATH
10:36 Save the changes and exit
10:44 Open a new terminal for the changes to take effect
10:57 Test fastqc
11:31 Test fastqc with an example data
11:40 Download the example data
13:05 Test fastqc using graphical interface
20:51 Test fastqc on the commandline

quality control of sequence data
fastq files
QC bioinformatics
Quality control bioinformatics

Keywords
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bioinformatics

#bioinformaticsforbeginners #bioinformatics #bioinformática #linuxforbeginners #linux

[ashamerin]

hi, im trying on Mac OS, it comes as dmg. then when trying to open it shows can't open as developer not verified. pls help

[mathildevarrault]

Thank you so much for this perfect and so simple to understand video !

[aymankhalifa]

when I tried to run these commands (chmod +x FastQC/fastqc & FastQC/fastqc --version), they didnt work, It seems I need a permission
I got (Can't open perl script "FastQC/fastqc": Permission denied)
I stopped at the fourth minute, I cant proceeds.
Could you help please ?

[isaacmengele]

Hello, the video has been very useful to install Fastqc, but the GUI doesn't show up, it seem some functionalities for GUI did not install. The analysis is done perfectly, how can I visualize the html files if GUI isn't working?

[cristianjaviermena]

muchas gracias!
^crack^ means ^genius^ in my country. thanks!

[koketsomakua]

I keep getting this error code. May you please assist

Exception in thread "main" java.awt.HeadlessException: No X11 DISPLAY variable was set, or no headful library support was found, but this program performed an operation which requires it, at at at at at at at