Interpretation of Output files from PICRUST analysis

[Kruttika Phalnikar]

Dear all,

I have recently started analyzing my data with PICRUST for KEGG ORTHOLOG and PATHWAY predictions.

I have processed my data as follows:

--Open reference OTU picking using QIIME

--Filtering OTUs to create close reference biom table

--Normalizing the above biom table for 16s copy number

Then, I use this ormalized table for the following commands:

predict_metagenomes.py -i otus_corrected.biom -o ko_predictions.biom

biom convert -i ko_predictions.biom -o ko_predictions.txt --to-tsv --header-key KEGG_Description    

categorize_by_function.py -i ko_predictions.biom -c KEGG_Pathways -l 3 -o pathway_predictions.biom

biom convert -i pathway_predictions.biom -o pathway_predictions.txt --to-tsv --header-key KEGG_Pathways

I get two text files KO_predictions.txt and pathway_predictions.txt

I have attached sample screenshots of my tables here

I am a little confused regarding the interpretation of the values given in these tables.

For instance, in KO/pathway predictions, do numbers indicate total number of genes which correspond to a particular protein/pathway or something else?

I tried to read about it, but could not get the exact answer

Sorry for such a basic question!

Thank you,

Kruttika

[Kruttika Phalnikar]

Thank you so much !!

[Gavin Douglas]

You're welcome! 

I see my reply wasn't posted to this group, so I pasted it below in case anyone else has the same question:

The KO table is made by multiplying the normalized OTU abundance by the number of KOs in each predicted genome.
The pathway table is made by collapsing the KO categories to the pathway level. In other words, we count up each pathway that each KO is involved in. Since genes can be involved in multiple pathways this means that the count of pathways will be greater than the counts in the KO table.

[junai...@admin.muet.edu.pk]

Thanks for your answer...

May I may ask for a little more favor. How did plotted the results. Did you selected particular predicted KEGG IDS and pathways according to your need or what?