Hello,
this is my first time working with QIIME2 and 16S data, so I might be missing something basic.
I’m analyzing Illumina data. I imported the data and obtained the following:
I was wondering if I should be using denoise-single instead of paired-end since the reverse reads look so bad?
Thank you very much for your time. Really apreciated it
Hello Maialen,
Welcome to the forums! 
You are asking all the right questions! Yes, you can use denoise-single on paired-end reads if R2 has too low quality.
Which 16S region did you sequence? I ask because depending on the length of this region, you may have enough coverage where you can still use both reads with some appropriately short trimming settings for R2.
Hello, thank you for your response. I sequenced the V3-V4 region. From what I understand, this region is quite long, so you really need both reads in good shape to get enough overlap for merging. In my case, R2 drops in quality so fast that, even trimming it short, the overlap becomes too small to merge reliably. That’s why I’m considering using denoise-single on R1 only…
Does that make sense in this situation?
Thank you very much again.
Sure!
R1 should cover all of the 16S V3 region and that's a simple path forward.
