Hi, I'm trying to build a mouse microbiome model using micom-q2.
But the AGORA file that micom tutorial provided don't have some genus included in my mouse metagenome sequences data.
So I want to make a genus metabolites model, and there's some questions.
What's the genus model? I mean, there's a lot of species in one genus classification. What species is included in the genus metabolite model? The whole? or The choose one?
Then, how can make a genus model? I have the original AGORA files(GitHub - VirtualMetabolicHuman/AGORA: The aim of this repository is to maintain, refine, and expand the AGORA collection of genome-scale metabolic reconstructions for human gut microbes through the use of issues. Please note that pull requests will be automatically closed.) classified species level.
- If I have to merge the species files for one genus metabolite model, the reactions and metabolites from different species are all included? or selected?
- If I have to select the reactions or metabolites, what criteria do you choose?
- What's the tool that I can use for the merge?
Please let me know the way to make the genus metabolites models.
I'll be waiting for the reply. Thanks!