Question: How to rarefying 18s rDNA data?
0
gravatar for 1713307477
5 months ago by
17133074770
17133074770 wrote:

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?

sequence R • 162 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by 17133074770

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.

ADD REPLYlink modified 5 months ago • written 5 months ago by N15120

If i want to plot a rarefaction curve, should i plot it before rarefying the otu table or after?

ADD REPLYlink written 5 months ago by 17133074770

You plot it before rarefying. I suggest following tutorials to do this:

https://rpubs.com/brouwern/iNEXTvVEGAN

ADD REPLYlink written 5 months ago by N15120

Thank you for your reply.

ADD REPLYlink written 5 months ago by 17133074770
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