FastQC(2)

We need to run fastqc with the following command:

fastqc

and with the following options:

What? parameter Our value
The input directory positional ~/workdir/data_artic/basecall_tiny/ or ~/workdir/Illumina/*.fastq.gz
The output directory -o ~/workdir/fastqc/basecall_tiny/ or ~/workdir/fastqc/illumina/
The number of threads to be used -t 14

Go to your workdir fist:

cd ~/workdir

Then create folders for the results (fastqc will not create them):

mkdir -p ~/workdir/fastqc/basecall_tiny
mkdir -p ~/workdir/fastqc/illumina

The run fastqc for Illumina data and on Nanopore data:

fastqc -t 14 -o ~/workdir/fastqc/illumina ~/workdir/Illumina/*.fastq.gz

fastqc -t 14 -o ~/workdir/fastqc/basecall_tiny ~/workdir/data_artic/basecall_tiny.fastq.gz

After that, you can load the reports in your web browser. Open a file browser, go to your workdir/fastqc/ directory and double click the html file. Or use the command line:

firefox ~/workdir/fastqc/illumina*.html

firefox ~/workdir/fastqc/basecall_tiny/*.html

Look out for the differences between Illumina data und Nanopore data. Is there Addapter contamination in your read data?

You should also check out the FastQC home page for examples of reports including bad data.

Note: When you run fastqc without “-o”, the results of fastqc are located in the directory that contains the reads.

So the first bases may indicate an adapter contamination. For workflows including de novo assembly refined with nanopolish or medaka adapter trimming is not necessary, but in other workflow scenarios this can be important to do and good there are tools which can handle this, as e.g. porechop.