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Ah, good to know! The QuantSeq manual/FAQ doesn't indicate whether or not deduplication is necessary (below is a screen shot of their recommended trimming), but my data is single-read without UMIs, and from a couple things I've read online deduplication isn't recommended (or possible?) for this type of data. Let me know if you think otherwise!
Recommended trimming according to QuantSeq's FAQ:
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Hi Misha-
I used your pipeline back in fall 2018 on some pilot QuantSeq data, at the suggestion of a colleague. It worked well then, but I don't think you had incorporated deduplication yet (?). I will probably depart from your process a bit, now that I more fully understand what your pipeline is intended for. I will align data to the Olympia oyster (Ostrea lurida) genome, which my lab developed.
Regarding deduplication, that's interesting to know, and I'll definitely have to do more reading on the matter. I'm now wondering if there is a tool I can use to identify duplicates based on the read sequences themselves (i.e. identical sequences), despite not having paired data or molecular identifiers... if you know of any, please let me know! Thanks for all you help!
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