I have problem in the trimming my RNA seq reads. The problem is that although the length of all reads are the same, 101 nucleotids, quality test by fastqc shows some reads contain adapter (adapter content is red). For reads containing adapters, I trimmed them by Trimmomatic using ILLUMINACLIP command resulting in the adapter removal. My problem is for some other reads that I can not understand if they contain adapter or not because the adapter content in fastqc file is yellow and according to adapter content graph, from 12th or 13th nucleotide, it seems something wrong because before 12th nucleotide, the graph line is completely direct. I trimmed the reads according to mRNA-Seq Library Prep Kit V2 Lexogen protocol as "The first nine nucleotides need to be removed from Read 1 (starter side), while on the stopper side it is only six nucleotides (Read 2)." But fastqc test shows the same result as before and the problem still exists. So I got completely confused. Would you pleas help me to trim these reads?