Import PICRUSt2 Multiplication Table

The Import PICRUSt2 Multiplication Table (beta) tool can be used to import multiplication tables from PICRUSt2 [Douglas et al., 2020] in order to perform functional inference for OTU abundance tables using Infer Functional Profile (beta) or to normalize OTU abundance tables by rRNA copy numbers using Normalize OTU Table by Copy Number (beta).

Before running the tool it is necessary to download the relevant data files from the PICRUSt2 github repository (, specifically three kinds of files are required:

  1. Files with 16S, 18S or ITS sequence alignments
  2. Files with rRNA copy numbers
  3. Files with functional term counts associated with each type of rRNA

Only files corresponding to the same rRNA regions can be combined to obtain a valid PICRUSt2 Multiplication Table, e.g. 16S alignments for prokaryotes, 16S rRNA counts and COG terms associated with 16S regions in prokaryotes.

Note that the rRNA copy numbers for fungi 2 are not consistent for 18S and ITS regions, which may have implications for the normalization and thus also for the functional inference for fungal data.

The tool can import similarly prepared data if other data sources are available. The OTU sequences need not be aligned.

To run the tool, go to:

        Toolbox | Microbial Genomics Module (Image mgm_folder_closed_flat_16_h_p) | Databases (Image databases_folder_closed_16_n_p) | Functional Analysis (Image functional_analysis_folder_closed_16_n_p) | Import PICRUSt2 Multiplication Table (beta) (Image import_multiplicationtable_16_n_p)

In the tool dialog (figure 18.10), select which type of rRNA and which type of terms you would like to import, then select the corresponding three files downloaded above where

Image import_picrust_wizard1
Figure 18.10: The Import PICRUSt2 Multiplication Table (beta) tool options.

After import the data in the multiplication table is displayed in a table (figure 18.11) where the name of the rRNA is given under the "Assembly" column, as these tables are typically derived from assemblies with known rRNA content, taxonomy and functional counts. The following four columns list the rRNA copy numbers registered for each type of rRNA, ITS regions will be listed as the selected rRNA type, e.g. 18S or 28S and the number of distinct funtional terms registered for that assembly in the column "Number of terms".

Image picrust_multiplication_table
Figure 18.11: The PICRUSt2 Multiplication Table visualization. When selecting one or several rows in the upper table, the lower table will show the combined functional counts for the selected row for each of the functional terms individually.