Greetings and salutations, I am attempting to analyse some human Illumina WXS data and am getting some unfamiliar kmer over-representation. Usually post trimming (trimmomatic) I get quite good removal of kmers but with this latest data I can't seem to get rid of the 3-primer kmers. My question is in two parts.
1) Should I worry about this or just continue alignment/variant calling.
2) If I should worry about, how can I trim these successfully?
My trimmomatic parameters and pre/post trimming images are below, but I am probably missing something super obvious.
Thanks in advance.
trimmomatic-0.36.jar -phred33 1_ATGCCTAA_L001_R1.fastq.gz 1_ATGCCTAA_L001_R2.fastq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:adapters/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:75