GAGE Pathview

• After processing the HMM files MetaCerberus calculates a KO (KEGG Orthology) counts table from KEGG/FOAM for processing through GAGE and PathView.
• GAGE is recommended for pathway enrichment followed by PathView for visualizing the metabolic pathways. A "class" file is required through the --class option to run this analysis.

Tip

As we are unsure which comparisons you want to make thus, you have to make a class.tsv so the code will know the comparisons you want to make.

For example (class.tsv):

Sample	Class
1A	rhizobium
1B	non-rhizobium

• The output is saved under the step_10-visualizeData/combined/pathview folder. Also, at least 4 samples need to be used for this type of analysis.

• GAGE and PathView also require internet access to be able to download information from a database.

• MetaCerberus will save a bash script 'run_pathview.sh' in the step_10-visualizeData/combined/pathview directory along with the KO Counts tsv files and the class file for running manually in case MetaCerberus was run on a cluster without access to the internet.