Introduction

The Choose taxonomic level task allows you to generate a count matrix summarizing the number of reads that have been classified by Kraken for each taxon, 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 count data. 

Running the Choose Taxonomic Level Task

The task can be performed on a Taxonomic data node, which is the output from a Kraken task.

• 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 
• Click Finish

Download a count matrix

Downstream Analysis