Good day! I am new to QIIME2-2019.1 I am stuck with the denoising stuff. I am not sure about the trim/trunc length. I have read multiple forum yet I couldn't decide the parameters. I am currently doing 16S V3-V4 region of MiSeq data. Any tips? Thank you. [Screenshot%20from%202019-04-20%2011-22-18…

Hi @RCM , Wow, those are some really nice quality plots! I'd say your sequencing run went very well. Which is really good since the V3-V4 region is fairly long and can be hard to hit (depending on your specific primers I think you only have about ~90 bases free after 2x300 sequencing for that regio…

Oh and make sure you trim off your forward primer's length with trim-left. That may cover the slightly lower quality on the start of the read (which is very normal), or if your lower quality is a bit longer, go ahead and extend the trim-left a few more bases.

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Tips in trimming and truncation length

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