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
Figure 1. Choose taxonomic level task set up page. Check one or more boxes
Download a count matrix
Downstream Analysis
Additional Assistance
If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.
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