I'd like to continue from my previous discussion on ASVs having the same species more than once: ASV data having same species more than one. I have some remaining doubts about ASV data that @cherman2 has already clarified.
My PI asked me how to analyze this data. First, we need to check the top 10 abundant species. Here is my question: How can we visualize the top 10 abundant species using ASV data? In the ASV data, we can see that the same species appears more than once in the top 10 species. How can we analyze this?
Question 2: Should I include all species (same species) for alpha diversity and beta diversity analysis?
Question 3: Does Qiime2 have any plugins that can be used to generate OTUs at a similarity threshold of 97%?
It can be done with taxonomy barplot - you can select it directly in the taxonomy barplot visualization. Abundances of all ASVs from the same taxa level will be summarized before convertion to relative abundances. Moreover, asv table can be easily collapsed to any taxonomy level if needed. But be careful with species level - neither ASVs or OTUs from 16S data are providing reliable species level annotations.
It is better to calculate diversity metrics with your ASV or OTU tables rather than with collapsed to taxonomy level data.
In the Qiime2 docs check VSEARCH plugins, or look for the tutorials how to cluster ASV table to OTUs. It can be done with Dada2 output.
To get more reliable result we should do analysis at Species level or at strain level which will give more weight to our research. This is the reason behind we want to do the analysis at species level.
Please can you send me that tutorial which will cluster ASV table to OTUs?
Here is the link. Some additional steps can be implemented to remove chimeras, perform QC and remove primers. Also, it is possible to cluster ASVs to OTUs after Dada2.