HI, I have paired end sequences, when I do QC on my forward sequences, it showed overrepresented sequence indicating that as an adapter. TruSeq Adapter, Index 9 5’ GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTG However, in the reverse sequences are totally good. The scenario is that usually we have to trim the overrepresented sequences. So I have tried to trim it by Cutadapt using similar to this command line cutadapt -a AACCGGTT input.fastq > output.fastq Cutadapt has removed these sequence but I got bad sequence and I lost huge data.
My question is that is this Ok about losing huge data. Also, where if did not trim the overrepresented sequence will affect my mapping later on?