trim_galore auto-detecting Illumina adapters

Question

[irritable_phd_syndrome]

I am fundamentally confused about how RNA-Seq is done with the Illumina HiSeq technology. I previously thought that random hexamers on the flow cell were used to bind to fragments of RNA and were then sequenced. However, I recently started using trim_galore and it auto-detects the Illumina adapter, AGATCGGAAGAGC, which is not a hexamer nor is it random.

In what step does this adapter get introduced in the library preparation? Also, any additional graphics / explanation regarding library prep would be much appreciated.

[h.mon]

Try this link. Two of the first hits are this and this.

edit: you will find adapters when your insert size is shorter than the length of the sequencing read.