I used trimmomatic to remove adaptor sequences and sequences less than 36bp from my RNA-seq reads. At first I used TruSeq 3 adaptors that came with the trimmomatic binary but this didn't remove much at all. I then used the TruSeq3-2 adaptors which removed nearly everything, but unless my eyes are playing tricks on me, on the "adaptor sequences" graph I can still see a tiny red line indicating "Illumina universal primer" at position 85 on the read. As the reads are 85bp long, does this indicate that I have just 1bp of adaptor sequence left in my reads? If so, is this anything to worry about? As FASTQC didn't highlight any specific primer sequence I spotted this presence of adaptors using the graph and I made an educated guess it would be TruSeq3 so I'm not sure how I'd go about spotting which specific primer I have in my sample.
Many thanks for your help as always
EDIT: I should probably add my sequences are Illumina HiSeq 2X100bp PE reads