STAMP example

There are many possible ways to analyze PICRUSt2 output. STAMP is one tool that can be used that requires no background in scripting languages. This tool is very useful for visualizing microbiome data, but note that there are much better alternatives for conducting statistical tests with compositional data (such as the ALDEx2 R package).

1: Install STAMP (this has to be installed on a local machine, not a server since it has a graphical interface).

• Windows: Download and install.
• Mac or Linux:

conda deactivate
conda install -c bioconda stamp

Then simply type the following to start (try STAMP if the below command fails):

stamp

2: If you ran the PICRUSt2 on a remote server you will need to download and uncompress the files you are interested in exploring (e.g. path_abun_unstrat_descrip.tsv.gz and metadata.tsv from the tutorial) to your own computer. You can use WinSCP (for Windows) or CyberDuck (for Mac).

3: Start up STAMP and load in the the uncompressed prediction table (e.g. path_abun_unstrat_descrip.tsv) as the Profile File, and the metadata file (e.g. metadata.tsv) file as the Group metadata file. You can now explore the data overall with heatmaps and ordination tools like PCA or alternatively compare boxplots of the relative abundance of individual predicted pathways.