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Old 10-22-2013, 02:44 PM   #2
atcghelix
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Location: CA

Join Date: Jul 2013
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What are you sequencing? And are you sequencing paired-ends?

As I understand it tools find "PCR duplicates" by comparing mapping coordinates of reads. However, if in your library prep you have actual fragments that shear in the same place then the resulting reads will also map to the same location. So they'll look like PCR duplicates in that they map to the same spot on the reference, but they actually represent good, unique reads.

The probability of this happening will increase with smaller references (smaller genomes, RNA-seq, targeted enrichment sequencing). The probability should decrease greatly by using paired-end reads as well, as the fragments in the library then have to shear at the same location at each end of the fragment.

I don't know if there's a standard protocol, but I'd be inclined to filter out the optical duplicates and leave in the "PCR" duplicates in your case.
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