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Quality Control

The first stage in our analysis is to undertake some basic quality control analysis on the reads.  To do this we will use the fastqc program from the Babraham Insititute:

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

To start we will create an output directory for fastqc in our home directory:

cd ~/ngs

mkdir fastqc

Firstly we need to load the required Raven modules to run fastqc

module load java

module load fastqc

Before running fastqc in command line mode and outputing the results into our newly created directory:

fastqc -o fastqc/ Brca1Reads_1.1.fastq

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We can review the text output using by unzipping the output and then using less:

module load p7zip

7z x ./fastqc/Brca1Reads_1.1_fastqc.zip -o"fastqc"

less ./fastqc/Brca1Reads_1.1_fastqc/fastqc_data.txt

Now repeat these tasks for the Brca1Reads_1.2.fastq file.

If you are able to work out how to transfer the /fastqc/Brca1Reads_1.1_fastqc.html back to your local machine, you can get a graphical overview of the quality of your fastq file.