Hi all,
I'm using Blast2GO to conduct functional analysis of DEG's from my RNA-seq experiment. I've ran through the workflow (Blast, Interpro, Mapping, Annotation, etc). Right now I would like to conduct enrichment analysis through the Blast2GO platform which uses a Fisher's Exact Test.
My question here is do I need to annotate the entire reference transcriptome of my organism in order to run the enrichment analysis here? The tutorial on the Blast2GO website isn't super clear to me...plus I'm pretty new to all of this! But it appears I have the first part done (genes annotated w/ GO terms) but now I need another input file (it says test file and then an optional reference file) in order to run the enrichment analysis. Essentially, I have multiple comparisons between different treatments and they all have different compositions of DEGs. I want to run enrichment analysis for each of these comparisons (10 in total) but again I'm not sure what exactly my other input file should be...my organism of interest is Ostrea lurida which isn't super well-annotated but I have the reference transcriptome on hand.
Thanks in advance,
Aaron
