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trim_galore auto-detecting Illumina adapters

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.

rna-seq trim-galore
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updated by Ram Ram • written by irritable_phd_syndrome • irritable_phd_syndrome

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.

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written by h.mon h.mon

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