Hi, Does Dada2 automatically reverse complement the reverse reads or do I need to do that before the denoising step? My reverse reads were provided to me in the forward orientation. I was not able to find that in the original Dada2 paper or anywhere else. Thank you for your help.
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Hello Claudia,
Yes! You can pass in your reads exactly as they come off the Illumina sequencer.
Bonus: here's the line in the dada2 pairing script where the reverse read gets rc() reverse complemented:
Colin
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Thank you very much much for your response! I will run it without reverse complementing first. However, your script doesn't correspond to the one Im using from qiime2:2019.10. which doesn't have the reverse complement part (rc) that you show here. So, I am still wondering if this qiime2 version automatically reverse complement the reverse reads or not. Any ideas?
Hello Claudia,
The script I posted is part of dada2, which is called by the the Qiime 2 plugin q2-dada2, which is included in qiime2:2019.10. So while this is not the same script you are running, this exact line of code is being run when you denoise your data.
It's Qiime2, calling Dada2, calling rc()
It's code, calling code, calling code
It's turtles all the way down 
Colin
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