My FASTQC raised three errors. Per base sequence content, per sequence gc content, and sequence duplication levels. I read that this could be because adapters have not been trimmed. I tried using Trimmomatic to trim adapters but I'm not sure that I did it correctly. I used Illuminaclip and tried both TruSeq3 options, I also did slidingwindow averaged bewtween 4 bases with a cutoff score of 20. The sequencing lab sent me a text file of the adapters and I tried cutting and pasting it in as a custom adapter but received an additional sequence length distribution error when I ran the FASTQC. Here's the text file contents: (I removed the > symbols because they were making the post weird but they preceded each "Adapter")
Is this dual indexed?