You can use FastQC to get a sense of your data quality before alignment:
Video Tutorial here:
Try to run FastQC on your fastq files:
cd $RNA_HOME/data fastqc *.fastq.gz
Then, go to the following url in your browser:
- 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
Exercise: Investigate the source/explanation for over-represented sequences:
- HINT: Try BLASTing them.
PRACTICAL EXERCISE 4
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’.
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 does the Adaptor Content warning tell us?
Solution: When you are ready you can check your approach against the Solutions.
Run MultiQC on your fastqc reports to generate a single summary report across all samples/replicates.
cd $RNA_HOME/data multiqc .