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I'm really newbie in 16s microbiome analyses, so sorry for this question. I would like to perform a meta-analysis using only Illumina Amplicons sequences from different studies that have different design. Specifically, I want to understand if is it possible to combine together V1, V3, and V3-V4 sequences. If yes, can DADA2 pipeline be used straightforward, or are preliminary operations needed? Since I'm an R user, please suggest libraries accordingly if possible.

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  • $\begingroup$ Hard to say based on available information. Are the different sequences collected on the same samples? Or different sequences on different samples? If the latter, I don't think that there is a robust way to combine that data, sorry. If the former, there might be, but I don't know it and I would use it with caution. I might trust comparisons between samples assayed with the same sequence but not throwing everything into the same bucket. $\endgroup$ Mar 26 at 22:09

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