How to rarefying 18s rDNA data?
I have one raw otu (without rarefying) about 18s rDNA from ocean samples. I only want to analyze the alpha and beta diversiyt of phytoplankton based on otu table, so i extract them from otu table. And now, my question is that should i firstly rarefy my otu table before extract phytoplankton from this table and for later alpha and beta diversity, or should i firstly extract phytoplankton from these this table and then rarefy this table for later alpha and beta diversity? Can anyone gives me some suggestions about that?
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I think you should rarefy first and then subset
The goal of rarefying is to even out samples with respect to different sequencing depths. So, I think it makes the most sense to “normalize” and then subset the organisms that you are interested in.
If i want to plot a rarefaction curve, should i plot it before rarefying the otu table or after?
You plot it before rarefying. I suggest following tutorials to do this:
https://rpubs.com/brouwern/iNEXTvVEGAN
Thank you for your reply.