How to interpret the 'qiime feature-table core-features' output

[Victor_Blasco (Victor)]

Hello everybody!

I want to define the core microbiome across my samples using the command 'qiime feature-table core-features'. Once I get the output, I upload it to "Qiime View" and it allows me to download multiple TSV files with lists of microbes, depending on the threshold I choose to consider an OTU part of the Core microbiome.
Once I download the TSV file I choose (this one, for example: core-features-0.850.tsv (78.1 KB)), this file contains multiple columns, with the following column titles:
1st column: "Feature ID"
2nd column: "2%"
3rd column: "9%"
4th column: "25%"
5th column: "50%"
6th column: "75%"
7th column: "91%"
8th column: "98%"

The first column contains the IDs of the OTUs that are part of the core microbiome. The other columns contain decimal numbers that are supposed to be "total percentile frequencies".

I do not understand why there are multiple columns with percentages as their title. Additionally, I do not fully comprehend why the frequencies change along the columns, and what they really represent.

Can anybody help me?

Thanks in advance

Victor

[colinbrislawn (Colin J Brislawn)]

Welcome to the forums, Victor!

Yeah, those columns are not mentioned in the docs for qiime feature-table core-features

Those are counts at various percentiles. Full explanation here.

Understanding QIIME2 core-feature TSV

Hello @Dharitri, Sure! Let's start with the file name: core-features-1.000.tsv This file lists the core features that appear in 100% of your samples. (There should also be other files, like one called core-features-0.700.tsv that lists features in 70% of your samples). You now have a list of taxa that appear in all your samples. If that's all you need, you can stop here. But... you might have more questions, like "these taxa are in all my samples, but how abundant are they across all my s…

Let us know if you have questions!