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Old 04-02-2019, 05:07 AM   #8
Location: Canada

Join Date: Jun 2013
Posts: 56

I will just echo cmbetts in saying that you should always remove your oligo/primer sequences from Sanger and High-throughput sequencing data since they are artificial. You can sometimes find primer/oligo sequences in "cleaned" sequences archived in GenBank and other public databases but this is not a good practice.

The only good reason I can think of off-hand to not trim the oligos is if you are archiving the raw data, in which case you should state the oligos used so others can trim them for downstream analyses.
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