PreAlignment QC
#1-vi. Pre-Alignment QC
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:
- http://YOUR_IP_ADDRESS/workspace/rnaseq/data/
- Note, you must replace YOUR_IP_ADDRESS with your own amazon instance IP (ex. 101.0.1.101))
- Click on any of the *_fastqc.html files to view the FastQC report
##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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