I have an OTU biom file (obtained from Closed reference QIIME 1.8.0 v) contains 65 samples, I am trying to do analysis for PAN/CORE genome.
I have filtered out the taxonomy from the abundance file (with particular threshold, lets say 60 %), now i have an taxonomy column only in file from all the 65 samples (with threshold 60%), Is there is a way where i can do the functional annotation for it ?
Any server/ software is there which can do that ? or which do pan (complete) /core (shared) analysis
Any suggestions ?
If you used GreenGenes 13_5 as a reference database, you can associate the OTUs with protein content of nearest sequenced reference genomes with PICRUST. However, in my opinion this approach is pretty much worthless. The 16S sequence of your OTU representative being relatively similar (60% is not even remotely similar, threshold should be like 99.9% for this stuff) to the 16S sequence of some reference genome does not mean that that the protein contents of these two genomes are even remotely similar..