Obtaining Rarefaction data


Can I know a method to obtain the rarefied data? I want to get a list of the observed features that survived the rarefying step.

Thank you in advance.

As I understood, you want to obtain a list of features that were retained after rarefaction while computing core diversity metrics. If I am correct, you should be able to find rarefied table in corresponding output folder. It can be visualized or exported to biom and then to .tsv to take a look on survived features.

Thank you @timanix for your response!
I used the following code to generate my rarefaction curve.
qiime diversity alpha-rarefaction
--i-table table.qza
--p-max-depth 15000
--p-metrics shannon chao1 observed_features
--o-visualization alpha-rarefaction4.qzv

I didn't get an output folder as you mentioned.

Oh, I thought that you already run core-metrics plugin to obtain alpha and beta diversity metrics.

It can be a little bit confusing, but the whole purpose of alpha-rarefaction plugin is to choose optimal depth for rarefaction, not to rarefy the data. Rarefaction itself is a random process, and every time you run it it will produce different outputs - so there is no way to predict which features will survive rarefaction (of course it depends on feature abundances but there will be differences anyway).

Rarefaction itself can be performed while computing core-metrics (sampling depth parameter) or by qiime feature-table rarefy plugin.

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Thank you! @timanix

I have plotted a rarefied table using the following command;
qiime feature-table rarefy
--i-table table.qza
--p-sampling-depth 15000
--o-rarefied-table rarefied-table.qza

qiime metadata tabulate
--m-input-file rarefied-table.qza
--o-visualization rarefied-table.qzv

Can I know why my rarefied table shows more than 8000 different species but my taxonomy.csv has only around 1000 different species? (I expected my rarefied table to have a less number of different species compared to the taxonomy.csv)

Your feature table contains ASVs (unless you collapsed your feature table at species level), not species (ASVs do not represent a species concept). Numerous ASVs may be assigned to one species, for example. So, number of ASVs is not equal to the number of species.

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By ASV, do you mean the id assigned to each sequence?

I have collapsed my feature table in species level.

My concern is, i have obtained a rarefied table for 26 samples. And the total amount of IDs generated are around 8000. And each of these IDs have various amounts of abundances (if as you said, several IDs could represent a single species, shouldn't the abundance of a single ID be 1?) However, the taxonomy table i have received has only 1124 different species.

I also want to know a method for me to merge my rarefied table and toxanomy data.


Is there a way for me to rarefy in taxonomy table instead of my feature table?

Thank you in advance,

Could you visualize your table and share it in .qzv format?

I think it is unusually high for the collapsed table. I am not sure that we are talking about the same things. Collapsed at species level table is a table that contains species level annotations instead of ASV IDs) and their abundances by samples.

No, they abundances should not be equal 1 (or I misunderstood you).

Species or taxonomy units? Some annotations can be not entirely complete.

You will need to collapse your rarefied feature table to certain taxonomy level (I am not sure if there is any point to rraefy table before collapsing).

Yes, you can collapse feature table to taxonomy level and then rarefy it.

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The rarefied table I have has the IDs and the abundances only. I want it to have the taxonomy units as well.

But 1 ID represents a single taxonomic unit right? (This statement is based on my assumption that 1ID represents 1 taxonomic unit , excluding abundances, but 1 taxonomic unit and be represented by several IDs as there can be more than 1 species having the same taxonomic unit)

I used the following plugin to obtain my rarefied table
The result i got has an ID column and the abundances of each ID in a sample. It doesn't have the assigned taxonomic annotations.

Thank you in advance,

That's mean it as an ASV table, not collapsed to species level.
Here you can read how to add taxonomy to the biom file or to collapse feature table.

Now I undesrtood - you mean that each ID should be unique, not the counts of one ID in feature table among your samples. It is right. But still, you are working with ASV table now, and they are not species. If you collapse your table to species level, each species should be unique in your new collapsed table.

Rarefaction is for subsampling, not for taxonomy assignment.

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