Hi guys, I have a question. After running fasqc, I've discovered that some of my reads has overrepresnted sequences as follow
fastq.R1 Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAACAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 141860 0.4972976921930607 TruSeq Adapter, Index 13 (97% over 40bp) NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 55712 0.19530134659142676 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAACAATCTCGTAT 50886 0.17838354973167975 TruSeq Adapter, Index 13 (97% over 40bp) fastq.R2 Sequence Count Percentage Possible Source GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 72457 0.2540018249205738 No Hit NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 61284 0.21483428569265142 No Hit
but the adapter content is perfect. I would like to remove those adapters or overrepresented sequences. I've never done that before in PE, so I'm trying to figure out. At that moment I'm trying:
cutadapt -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAACAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -a NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAACAATCTCGTAT -A GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG -A NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN -o out.1.fastq -p out.2.fastq R1.fastq R2.fastq
any one with experience could tell me if this is right?
Thank you in advance!