Step 1: Set up an account and import the necessary pre-calculated files
The CowPi workflow is provided free for use by the wider scientific community at Aberystwyth University. A full description of how to set up your Galaxy account, the work flow and how to import pre-calculated files is provided here: http://www.cowpi.org/p/setting-up-cowpi-on-galaxy-account.html.
Step 2: Upload your files to Galaxy.
You need a fasta formatted OTU file like in Figure 1 and a tab-delimited OTU count table for each of your samples as shown in Figure 2. Two example files are provided ‘timecourseOTU.fa’ and ‘OTU_Table.txt’.
Step 3: In the CowPi workflow, select the correct files for each step.
Choose the following options (as shown in :
Select the OTU fasta file (timecourseOTU.fa) in step 1 and enter country and institute information.
2: (Extract Names):
Select the OTU count data (timecourseOTU.fa).
4: (Convert BIOM)
Select the precalcuated 16S copy-number file (16S_precalculated.tab).
6: (Predict Metagenome)
Select the precalcaulted KO abundance files (ko_precalc1.tab).
Then click “Run Workflow”.