Happy New Year to all QIIME 2 developers and the community!
When I applied PICRUSt2 to my ITS data, I didn't generate the 'ko_metagenome_out' folder ; only ec_ITS_counts.txt_metagenome_out folder was generated. Is this normal?
Additionally, does it make sense to use MetaCyc pathway abundance to predict ITS functional analysis instead of KEGG pathways (since I didn't generate ko folder to convert it to kegg abundance as I did for 16s)?
What's the difference between these two databases ( kegg and metacyc) when performing exploratory prediction analysis of ITS please?
Apologies for the incredibly slow reply - I imagine I'm a bit late to be useful for @Sue, but figured I'd add this incase someone else came across it.
There are only EC number annotations and not KO annotations available for the fungal reference data set. I'm not exactly sure why this is because I wasn't the one that originally made the databases. I would preferentially use MetaCyc pathways over KEGG pathways because there is no way for us to update the KEGG pathways - the file that we use for mapping to pathways is from the last publicly available release of the KEGG database (2012, I believe - it is no longer released publicly), whereas the MetaCyc pathway mapping file was taken from HUMAnN2 more recently. If you have a subscription to the KEGG database then you would be able to use a more updated version for the KEGG pathways.