Download FastQC http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Unpack unzip fastqc_v0.10.1.zip
Check if you have java runtime environment JRE, above 1.6 or 1.7: java -version
Change permissions to fastqc: chmod 755 fastqc
Run FastQC: ./fastqc
This will run fastqc as a graphical interaction interface.
If you run it on a server, log in with: ssh -X
Choose file you want to analyze and run the analysis.
If you want to run it in a non interactive mode to analyze multiple files at once or to pipe it in a script use: ./fastqc filename1.fastq filename2.fastq filename3.fastq
Each file will be analyzed and an html report will be created and no interactive mode will be launched when you put the filename after ./fastqc
If you copy the executable file fastqc to a folder where you have your fastq files and try to run it with ./fastqc you will get this message:
Error: Could not find or load main class uk.ac.babraham.FastQC.FastQCApplication
as java cannot find the initial class file FastQCApplication.class that is located in the FastQC folder.
You may want instead to create a link in that folder to the fastqc file or place a link in usr/local/bin/:
sudo ln -s /path/to/FastQC/fastqc /usr/local/bin/fastqc