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

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


1 Like

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.

Let us know if you have questions!