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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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• Click a Taxonomic data node
• Choose Choose taxonomic level from the Metagenomic section of the toolbox
• Check one or more taxonomic levels. The options are Superkingdom, Kingdom, Phylum, Class, Order, Family, Genus, or Species (Figure 1). A separate output data node will be generated for each one that is selected (Figure 2)
• Click Finish

The choice of taxonomic level depends on which level you want to perform downstream analysis on and your research question. For example, if you want to know which families of bacteria are the most abundant in your sample, choose the family level. If you want to see which species are differentially abundant in different groups of samples, choose the species level.

Download a count matrix

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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 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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