Understanding QIIME2 core-feature TSV

[Dharitri (dharitri saikia)]

Hello there,
I am trying to find out the core taxa in my samples. for that, I ran "qiime feature-table core-features --i-table gut-table-with-taxa.qza --p-min-fraction 0.7 --p-max-fraction 1.0 --o-visualization viz

.core-gut-taxa". Could anyone pls make me understand what the percentage and the values against each taxon mean? I have gone through How to read core-feature TSV - #4 by Nicholas_Bokulich but it did not help me much.
Thanks in advance!

[colinbrislawn (Colin J Brislawn)]

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 samples?"

And that's what the columns show. Each column lists the count at a percentile.
The 50% column is the median count, a.k.a. Q2
The 25% and 75% columns are the 25th and 75th percentile, a.k.a. Q1 and Q3, a.k.a the Inter Quartile Range (IQR).

[Dharitri (dharitri saikia)]

Thanks again! @colinbrislawn You are awesome.