Hi everybody, I am new to RNA-seq field. We have compared two transcriptome: tolerant and susceptible potato cultivars, in two times: control and after stress. I found articles that do the annotation some with unique DEGs and others with all DEGs (common and unique) for each cultivar. We want to use Blast2GO but I don´t know if I have to do the annotation considering only "unique DEGs" or with "all DEGs" for each cultivar?. Thanks
I guess you are interested in doing a Functional Enrichment Analysis by comparing differentially expressed genes (DEG) of 2 potato cultivars against each other. This can be done with Blast2GO and the Fisher's Exact Test: https://www.blast2go.com
In your scenario you would need to have (or generate) the functional annotation (GOs) for the unique genes of each cultivar only because if you run the statistical test comparing two different lists (and not test vs. reference-background set) common IDs are removed from both lists since they do not add information to the analysis. You can load both "unique" lists in Blast2GO, run the annotation, combine them and then run the enrichment analysis on the combined project and the corresponding DEG ID list. This can all be done easily without leaving Blast2GO.
You can find a video for the Fisher test and many others here:
And the user manual here: http://docs.blast2go.com/user-manual
Hope this helps and answers your question. Best, S.