Hi, from my understanding the adapter sequences can only occur on the 3' side of the sequencing reads if there is a read through. Does this mean that when you open a Fastq file (either R1 or R2) to inspect, you should see the majority of them on the right side of the file? In my Fastq files the majority of the adapter sequences that I see are on the left side and they correspond to exactly half of the sequence followed by 6,7 "A"'s, and the rest of the sequence seem to have a lower quality based on the quality values. The trimmomatic program seem to be removing them but I am curious about their source. Thanks for your help.