Hello,
We need to analyze the main pathways of a list of ECs after QIIME2 and PICRUST2 analysis.
In Metacyc pathways, we can search the main pathways EC by EC.
However, we have a list of more than 5000 different ECs.
It will be exhausted to search the pathways EC by EC .
So how can we do to analyze to find the list of the main pathways for each 5000 ECs?
Thank you very much,
Sorry to resurrect this, but @gmdouglas, do you have any advice?
There are several possibilities! First, you could run MinPath (MinPath), which is what PICRUSt2 does to get the predicted MetaCyc pathways. You could also manually run the latest version of MinPath with specific mapping files you are most interested in.
I haven't tried this tool, but it could also be potentially useful: GitHub - jotech/gapseq: Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
You could also use a custom programmatic approach (e.g. a Python script) to cross-reference how specific ECs are to each pathway. For instance, you could do a quick check for whether there are some ECs that are found in only 1 pathway, which would mean that those ECs are a marker for that pathway potential (given that the mappings are complete), and also for the percentage of ECs per pathway that are present. This is very similar to what MinPath does though, so it would largely be a sanity check!
I am cc'ing @Robyn_Wright as she has taken over on PICRUSt2, and may have other thoughts!