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 :
1: (Usearch):
Select the OTU fasta file (timecourseOTU.fa)
in step 1 and enter country and institute information.
2: (Extract Names):
Change nothing.
3: (Rstep)
Select the OTU count data (timecourseOTU.fa).
4: (Convert BIOM)
Change nothing.
5: (Normalize)
Select the precalcuated
16S copy-number file (16S_precalculated.tab).
6: (Predict Metagenome)
Select the
precalcaulted KO abundance files (ko_precalc1.tab).
7: (Categorize)
Change nothing.
Then click “Run Workflow”.
Done.
