FastQC
We have our raw reads renamed and in our main working directory. We will run FastQC to check the reads quality. This analysis is quick and we will inspect the results visually.
If we type:
ls *.gz
FG113_1.fastq.gz FG113_2.fastq.gz FG35_1.fastq.gz FG35_2.fastq.gz FGIntype_1.fastq.gz FGIntype_2.fastq.gz KGD465_1.fastq.gz KGD465_2.fastq.gz zygia917_1.fastq.gz zygia917_2.fastq.gz
We can include the name of all those files in a name file:
ls *.gz > fastqcfiles
Now take a look on what is inside the fastqcfiles
:
cat fastqcfiles
FG113_1.fastq.gz
FG113_2.fastq.gz
FG35_1.fastq.gz
FG35_2.fastq.gz
FGIntype_1.fastq.gz
FGIntype_2.fastq.gz
KGD465_1.fastq.gz
KGD465_2.fastq.gz
zygia917_1.fastq.gz
zygia917_2.fastq.gz
Now let’s run FastQC on all the files using a loop:
Note
If you don’t have FastQC installed, please take a look in Installing Software
Let’s check and take note of the version we are using:
fastqc -v
FastQC v0.11.9
Using -h
or --help
we can check how FastQC works and the options available.
fastqc -h
And finally run the loop:
while read f; do fastqc "$f" ; done < fastqcfiles
Let’s take a look in the output:
FG113 FG113_2_fastqc.html FG35_1_fastqc.zip FGIntype_1.fastq.gz FGIntype_2_fastqc.zip KGD465_2.fastq.gz renaming.sh zygia917_2.fastq.gz
FG113_1.fastq.gz FG113_2_fastqc.zip FG35_2.fastq.gz FGIntype_1_fastqc.html KGD465 KGD465_2_fastqc.html zygia917 zygia917_2_fastqc.html
FG113_1_fastqc.html FG35 FG35_2_fastqc.html FGIntype_1_fastqc.zip KGD465_1.fastq.gz KGD465_2_fastqc.zip zygia917_1.fastq.gz zygia917_2_fastqc.zip
FG113_1_fastqc.zip FG35_1.fastq.gz FG35_2_fastqc.zip FGIntype_2.fastq.gz KGD465_1_fastqc.html acc zygia917_1_fastqc.html
FG113_2.fastq.gz FG35_1_fastqc.html FGIntype FGIntype_2_fastqc.html KGD465_1_fastqc.zip fastqcfiles zygia917_1_fastqc.zip
FastQC produces reports on html
and in .zip
format. We will use the html
files to inspect visually our results. You can open them in any browser in your local machine.
To understand how to interpret the results please check FastQC’s webpage
If you are running this pipeline in a server, here is a reminder on how to move files between servers and local machines: https://help.cropdiversity.ac.uk/file-transfers.html
Note
We will use FastQC two times in the pipeline: in the raw reads and after using Trimmomatic to check the trimming effects.
After inspecting the results, we are ready to the next step, which is to trim the raw reads and for that we will use Trimmomatic.