The Choose taxonomic level task generates 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.
The task can be performed on a Taxonomic data node, which is the output from a Kraken task.
To export the count matrix for a taxonomic level, select the output data node and choose Download data from the toolbox. You can choose to put the features on the columns or rows (Figure 3). The 'features' in this context are the taxa. For example, if a Phylum data node is downloaded, the features will be different phyla. The download will be a tab-delimited text file with read counts for each sample (Figure 4).