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cdanielmachado / smetana

SMETANA: a tool to analyse interactions in microbial communities
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Co-occurrent bacteria #19

Closed ntromas closed 3 years ago

ntromas commented 3 years ago

Hi, I would like to test which metabolites pathways are complemented (if there is) between two taxa that are highly co-occurrent and that have co-evolved. I produced .xml with gapseq (I did not use any medium ref as these bacteria were never cultivated). I then just run Smetana on the two .xml files with -d parameters. Would you recommend this approach? Thanks for you help&suggestion

Cheers,

Nico

cdanielmachado commented 3 years ago

Yes, that approach makes sense.

Best regards, Daniel

ntromas commented 3 years ago

Hi Daniel,

Thanks for your answer. So I played with -d and -g. I have a small community of different taxa (different phyla). I got pretty high MRO (>0.75) and even higher (>0.85) with co-evolved small community. However, I always got warnings like "Gene association for reaction R_rxn... is not DNF". Do you know if it is because I am using a gapseq models? Thanks for your help,

Cheers, Nico

cdanielmachado commented 3 years ago

Hi Nico,

That's not a problem since gene associations are not used in SMETANA.

Daniel

ntromas commented 3 years ago

Hi Daniel,

Thanks!