Good morning to everyone,
To complete a DE genes analysis, at the end of my pipeline (during which I adopted DESEQ2 and edgeR methods, to compare results), I'd like to perform a GO enrichment analysis.
My main problem is that the GO terms aren't available on databases online, since I'm using a genome which is incomplete and only partially annotated. I'd like to use GO terms from that one.
I've tried to use the function goana from R, which I slightly changed to make it accept an external database, but it isn't working on my specific results, like I explained here.
I was considering topGo but it seems quite hard to adapt it to this purpose... I'd also be interested in something similar for KEGG analysis (for which I had thought of kegga from Bioconductor, but I guess I'm going to have similar issues).
Any suggestions there? What could I use which is free (I'm not going to buy BLAST2GO). Thanks in advance!
What you need to do is create your own set of GO annotations by transferring annotations from annotated species using orthology.
This is similar to what I wanted to do in case there is no alternative. More specifically, I'm working on domesticated olive tree and I could try by blasting domestic olive tree genes against Olea europaea var. sylvestris ones, so that I could use the GO annotations of the latter once I know the correspondance between domestic genes and wild ones...
Cross-posted on Bioconductor ( https://support.bioconductor.org/p/129909/ ; https://support.bioconductor.org/p/129910/ )