Amplicon Based Data
Hi all,
I have amplicon-based data where the reads look like this:
forward-adapter + 4bp molecular tag + ligation arm (18-24bp) + sequence of interest + extension arm (18-24 bp) + 4bp molecular tag + reverse-adapter
I have both forward and reverse reads (R1 and R2) and they are pair-ended. How do I isolate just the sequence of interest?
Furthermore, I want to remove both PCR and optical duplicates using the 8bp total of molecular tags. How do I do remove duplicates?
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