Hi,

imprt them into the FastQC program. Go for "overrepresented sequences" there should be stated which adaptors are used.

FastQC only gave you warning when overrepresented sequences were in first 200,000 sequences. see FastQC documentation

Supposed read1.fastq and read2.fastq is the paired end data with 4 lines per read.

Download common Illumina adapters from https://github.com/vsbuffalo/scythe/blob/master/illumina_adapters.fa

Go through each adapter, e.g. sampling 1 million read1.fastq for truseq-forward-contam adapter:

cat read1.fastq | head -4000000 | grep AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | wc -l 
cat read1.fastq | tail -4000000 | grep AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | wc -l

If the above command output >100, then sampling 1 million read2.fastq for truseq-reverse-contam will output with similar number:

cat read2.fastq | head -4000000 | grep AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA| wc -l 
cat read2.fastq | tail -4000000 | grep AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA| wc -l

In reference to the comment above, i tried the following commands:

cat read1.fastq | head -4000000 | grep <Adaptersequence> | wc -l 
cat read1.fastq | tail -4000000 | grep <Adaptersequence> | wc -l

on my fastq file and got different output numbers (2731 and 1818 respectively).

What does this signify?

You can find the illumina adapters on the illumina website.