I ran picrsut and am now trying to determine KEGG pathway abundance in different levels using the predicted KO abundances. I tried with the following command but it says I need to input map file (KGEG_pathways_to_KO.tsv).
pathway_pipeline.py -i KO_metagenome_out/pred_metagenome_strat.tsv -o KEGG_pathways_out --no_regroup --map picrust2/picrust2/default_files/pathway_mapfiles/KGEG_pathways_to_KO.tsv
Where can I get this map file?
As I like to generate pathway abundances in different levels such as cellular process, metabolism, human diseases and environmental information processing etc., do you have any special suggestions for me? I like to hear your special advice.
Thank you.