FastQC with raw reads indicated contamination by adapter sequences at the 3' end. Running IlluminaClip from Trimmomatic seemed to help the issue but adapter sequences appear to remain at the 3' end of at the 125-150bp positions. Any advice on what is going on and how I can go about troubleshooting? Attached are the FastQC Kmer enrichment plots for the same read file, untrimmed, trimmed and trimmed with clip threshold lowered from 30 to 20 (palindrome setting).
TruSeq Universal Adapter
5’ AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
TruSeq Adapter, Index 6
5’ GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG
TruSeq Universal Adapter
5’ AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
TruSeq Adapter, Index 6
5’ GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG
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