I have paired-end WES reads and FastQC report shows adapter content error “Illumina Universal adaptor”. I read the Adapter_list.txt in the fastQC folder which says that the Illumina universal adapter can be summarized in the 12 bp fragment of
My question is should I use this sequence (
AGATCGGAAGAG) for both forward and reverse reads? or I should make a complementary sequence of
CTCTTCCGATCT for the reverse read?
cutadapt -a AGATCGGAAGAG -A AGATCGGAAGAG -o tr_R1.fastq -p tr_R2.fastq R1.fastq R2.fastq
cutadapt -a AGATCGGAAGAG -A CTCTTCCGATCT -o tr_R1.fastq -p tr_R2.fastq R1.fastq R2.fastq