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geraldinepascal / FROGS

FROGS is a galaxy/CLI workflow designed to produce an OTUs count matrix from high depth sequencing amplicon data.
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NA in Function Hierarchy in Picrust2 Frogs implementation #71

Open LafontRapnouilTristan opened 3 months ago

LafontRapnouilTristan commented 3 months ago

Hello,

Thanks for the amazing work on FROGS! I am currently trying to analyse some microbial datasets using your picrust2 implementation and I am a bit puzzled by the meaning of NAs in function "classification". I am using FROGS from a galaxy server.

For some observation with a Kegg identifier (e.g. K00113) I don't have the associated function classification.

image

Can you explain me why? Is that about prediction confidence or just a mistake? Using KEGG database I have about 42% of my observations that are tagged as NA while it goes down to 6% on the same dataset but with Metacyc.

Tell me if you need more info about how I proceeded. Thank you very much.

mariabernard commented 3 months ago

Dear LafontRapnouilTristan,

Sorry for the delay.

We are investigating how annotation are reported, but looking at the few exemple you mentionned, it seems that we reported only annotation that are associated with EC number (so corresponding to enzymes).

It seems that you are currently working in a French accademic laboratory. Please contact us at frogs-support@inrae.fr so I can share with you an updated annotation file with KEGG annotations.