I have a question regarding overrepresented sequences from FastQC report. I really appreciate for your replies in advance. Please see attached.
First, I am going to remove Illumina Single End PCR Primer 1 using cutadapt. After this, there are three TruSeq Adapters left. In fact, they share same sequences but just different length (69, 67, 65bp). In this case, can I just put the longest one among three as input then the rest two shorter ones are removed at the same time? Or should I do it the opposite way?
First, I am going to remove Illumina Single End PCR Primer 1 using cutadapt. After this, there are three TruSeq Adapters left. In fact, they share same sequences but just different length (69, 67, 65bp). In this case, can I just put the longest one among three as input then the rest two shorter ones are removed at the same time? Or should I do it the opposite way?
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