Determining core bacteria

Hi, i am trying to determining the core bacteria of my samples. as far as i know, we can determine the core bacteria with heatmaps that generate by the different of frequency of occurences from each bacteria in all habitats, just like did in these graphs.

(Source: Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species | Animal Microbiome | Full Text)
(Source; Redirecting)

however, i really don't know how they did it.
by the way here is some of my data,
OTU Table Genus.tsv (4.1 KB)

does anybody can help me, please?


Hello Rijal,

Take a look at this thread and the plugin feature-table heatmap for building a heatmap, and some of the functions that are helpful along the way.

For your first question, check out qiime feature-table core-features, which lets you identity the core bacteria with high prevalence across your samples without a heatmap.

Of course, let us know if you have any questions!
Colin :bird:

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.