1. File preparation and inspection

First you need to unzip all of your Illumina fastq read files. In order to do so, copy all zipped fastq-files into one folder and run the following command from within that folder:
gunzip *.gz
After all of your files are unzipped (the .gz at the end of the filename should now have disappeared), you can check the number of reads in each file with this command (run from within the same folder):
grep -c '^+$' *.fastq
We found that a read-count of at least 200,000 reads per file is preferable but even files with between 100,000 and 150,000 reads may yield some useful results. You will be able in the next step to select a read-count threshold for files you want to process further.