I have a question for you:
I have data from illumina sequencing from bacteria (16S), fungi (ITS1 & ITS2), AMF (18S) and eukaryotes (18S).
I did separated runs for each organisms (DNA extraction from soil, PCR with target primers and illumina run) and I am now processing the data.
Since I have read in some papers that other researchers are getting the microbial functions by plotting the sequences in some specific website (database), such as MG-RAST, I am wondering if I can do the same, also if I had not done a pure metagenomic work based on DNA extraction and direct sequencing. I would like to have your comments and suggestions.
Best regards, Elisa