I apologize in advance if this is an obvious and dumb question.
What is the PRECISE difference between a PCR duplicate
versus
A unique sequence?
I tried looking for it all over, but was unable to obtain a clear explanation. Now, my thought process is something like this.
A PCR duplicate is something which is right off from the NGS instrument. i.e., you look for PCR duplicates from your Raw Fastq file.
Whereas a Unique sequence is …?
If you have a sequence as
Read 1 - ATCGCCCTA
Read 2 - ATCGCCCT
Would these be TWO unique sequences? If so, what is the algorithmic THRESHOLD in Mothur Unique.seqs to call two sequences as Unique versus Non-Unique?
Thanks for the favor of a reply.