I am using the metnet plugin. I would like to understand the results produced by the plugin as I cannot really understand by reading the instructions or the paper. The results produced are a file containing reactions with the names rxnAGORAn for each sample and the names of some metabolic pathways in the other files produced. How can i use these files for another analysis using tools such as MetaboAnalyst and how can i create a file showing exactly which metabolites are found named according to KEGG naming for example?
Hi @Angeliki,
Welcome to the community! Thanks for reaching out! I am reaching out to one of the developers of this software to see if they have any insights.
@tblasco, I don't know if you are still supporting this software on the forum, but if you are, I wanted to get this on your radar.
Regarding KEGG naming, there is not currently any method within metnet to extract this information from the data. However, this information can be obtained from the source data of q2-metnet. If you check the different XX_metInfo.csv files of the data folder, you will see all the metabolites in each metabolic reconstruction and different database identifiers, when available. You might be able extract the KEGG identifiers by mapping your results into this file.
I have never used MetaboAnalyst before. Could you give me more details about what exactly do you need to run it?
@tblasco, one thought as I'm reading this post. Those files that you're referring to look a lot like what we would describe either as FeatureData or feature metadata. If you were to provide those files as feature metadata (see the metadata format description here) that would open up possibilities for users to work with other QIIME 2 tools and possibly make it easier to extract the kind of information that @Angeliki is looking for. If that's of interest, and it would be helpful to have some guidance on it, let me know and we can find a time to connect.
I found those files and matched the names of the metabolites with the rxn IDs for now, i will see about kegg. I wanted to use the results for an analysis in metaboAnalyst
community! Thanks for reaching out! I am reaching out to one of the developers of this software to see if they have any insights.