Hello, I am using MEGAN to analyze long-read metagenomic sequences from the gut microbiome. I first used Flye to assemble the raw reads, then used DIAMOND to blast aganist the NCBI-nr database to create the .daa files. When meganizing, I used the Megan Mapping database for both the taxonomic analysis to examine taxa at the species level and SEED to look at the functional pathways. The problem I am running into is I can export the functional SEED analysis as seedName_to_count but I am struggling to trace it back to the specific gene pathways and what taxa are contributing to each functional pathway. Is there a way to do this through MEGAN, or is there another approach I should be taking? Thank you!
There is a tool in MEGAN (MEGAN/tools/taxonomy2function). I’m not sure if this is what you’re looking for, or if you might need to delve into correlation analysis instead. Let me know if this helps, or if you have further questions.
Best,
Anupam