Fastqc Linux Install and Usage (Commandline & GUI)

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

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


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Materials
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fastqc documentation https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ https://github.com/s-andrews/FastQCfastqc download page https://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc

link to example data
https://www.ebi.ac.uk/ena/browser/view/SRR957824

How to install java
linux(openjdk): https://youtu.be/q9ZuBJVfAfU
windows(SE): https://youtu.be/vJtx3IaN81w
windows(openjdk): https://youtu.be/kISRCTzaaHc


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



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