I runned picrust2 full pipeline (
picrust2_pipeline.py -s study_seqs.fna -i study_seqs.biom -o picrust2_out_pipeline -p 4 )
The problem that I still can't understand the output files,

  • for example where I can find the Metacyc pathway abundance files outputs
  • Does EC used to determine Metacyc pathway abundance ?
  • difference between ko_metagenome_out pathways_out and EC_metagenome_out folders ( I have already read that EC_metagenome_out is Folder containing unstratified EC number metagenome predictions and * KO_metagenome_out is as EC_metagenome_out above, but for KO metagenomes.) but I still can't understand even what's unstratified EC number metagenome predictions
  • what's the difference between KEGG and MetaCyc abundances ?
  • Is it more interesting to conduct KEGG or MetaCyc downstream analysis ?

@gmdouglas Are you able to answer this picrust2 question? Thanks!

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@gmdouglas could you please answer my questions

Hi @Will_Ericksen,

I just wanted to jump in here with a quick reminder that we do not guarantee a response with tools outside of the QIIME 2 plugins that are managed by the core QIIME 2 development team. Gavin may not be available to address these questions, or may not be checking the QIIME 2 user forum on a regular basis.

Cheers :lizard:


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