I was wondering what the correct way was to get gene function from MAKER's outputs? I was hoping to upload the files to Blast2GO to assign functionality from Blast and Interproscan. The using Blast2GO, I wanted to create some visuals such as piecharts with gene family abundances, etc.
I tried doing this with both the .gff3 and protein.fasta outputs from Maker, but I could not get it to work in Blast2GO (It is very likely that I just do not know what I am doing).
Another source I found said to assign putative function using MAKER's post-analysis steps (http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Post_Processing_of_Annotations)
Once you do this which file do you upload to Blast2GO and run Interproscan? The GFF, protein or transcript?
Any advice on this or other functional gene assignment will be greatly appreciated!!