I have done gene set enrichment analysis which is now straight forward. Such as taking gene set and making a query. For microbiome data it is not that straight forward which I found out.
Step done so far..
- Ran Kraken2
- Generated OTU table
- Downstream analysis using phyloseq.
Now if I have to the functional enrichment from start I would need to use qiime2 which I didn't do earlier.
Now the other option after reading through paper I found kegg can also perform the microbiome functional enrichment
Unlike other database I'm not sure where do I put query in KEGG for the bacterial genus level whatever found.
Any suggestion how to proceed would be really helpful