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")
Adaptor1_5p GATCGGAAGAGCACACGTCTGAACTC
Adaptor2_5p AGATCGGAAGAGCGTCGTGTAGGGAA
Adaptor3_5p TTCCCTACACGACGCTCTTCCGATCT
Adaptor4_5p GAGTTCAGACGTGTGCTCTTCCGATC
Adaptor1_3p TTCCCTACACGACGCTCTTCCGATCT
Adaptor2_3p GAGTTCAGACGTGTGCTCTTCCGATC
Adaptor3_3p GATCGGAAGAGCACACGTCTGAACTC
Adaptor4_3p AGATCGGAAGAGCGTCGTGTAGGGAA
TruSeq-Universal_Adapter_5p AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
TruSeq-Universal_Adapter_3p TCTAGCCTTCTCGCAGCACATCCCTTTCTCACATCTAGAGCCACCAGCGGCATAGTAA
Is this dual indexed?
How to add images to a Biostars post
I made the changes for you this time so that images are displayed properly. You have to provide the full link to the image.
You would find it useful to read several blog posts by authors of FastQC that you can find them here:
https://sequencing.qcfail.com/articles/positional-sequence-bias-in-random-primed-libraries/
https://sequencing.qcfail.com/articles/libraries-can-contain-technical-duplication/
And the sequence length distribution error is due to the trimmed sequences won't have the same length as those untrimmed.