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_DNS_NAME/workspace/rnaseq/data/
• Note, you must replace YOUR_DNS_NAME with your own amazon instance DNS (e.g., ec2-54-187-159-113.us-west-2.compute.amazonaws.com))
• Click on any of the *_fastqc.html files to view the FastQC report

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PRACTICAL EXERCISE 3

Assignment: Run FASTQC on one of the additional fastq files you downloaded in the previous practical exercise.

• Hint: Remember that you stored this data in a separate working directory called ‘practice’.
• Hint: Use the same approach as above to get a copy of the fastq file on your local machine by downloading it from your cloud instance.

Run FASTQC on the file 'hcc1395_normal_1.fastq.gz' and answer these questions by examining the output.

• How many total sequences are there?
• What is the range (x - y) of read lengths observed?
• What is the most common average sequence quality score?
• What is the most common kmer that is observed?

Solution: When you are ready you can check your approach against the Solutions

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