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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Analysis complete for Brca1Reads_1.1.fastq
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.
