PreAlignment QC

#1-vi. Pre-Alignment QC

You can use FastQC to get a sense of your data quality before alignment:

• http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Video Tutorial here:

• http://www.youtube.com/watch?v=bz93ReOv87Y

Try to run FastQC on your fastq files:

cd $RNA_HOME/data
fastqc *.fastq.gz

Then, go to the following url in your browser:

• http://YOUR_IP_ADDRESS/workspace/rnaseq/data/
• Note, you must replace YOUR_IP_ADDRESS with your own amazon instance IP or DNS name (e.g., "cbw01"))
• Click on any of the *_fastqc.html files to view the FastQC report

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