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The Choose taxonomic level task generates a count matrix summarizing the number of reads that have been classified by Kraken for each taxon in each sample, at a given taxonomic level. The counts give a measure of the relative abundance of each taxon, which can be used for downstream analysis and visualization as if it were RNA-Seq gene expression count data. 

Running the Choose Taxonomic Level Task

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Downstream Analysis 

The taxon-level count data node(s) behave like any other count matrix in Partek Flow. This means you can perform most of the tasks you would normally perform on gene expression data. For example, you can normalize the species counts, perform principal components analysis (PCA), and use ANOVA to detect differentially abundant species in different groups of samples (Figure 5). Additional visualizations can also be generated including heatmaps, volcano plots, dot plots, and more.

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