I have a question for you about GO annotation of RNA seq data: I have differentially expressed genes (used Edge R to analyze RNA seq data) and I need know GO terms of those genes. I have GO terms for most of the transcripts and I got those GO terms (with IDs) directly from the reference genome I used for the analysis. I want to know whether those GO terms (got directly from the reference) are enough OR is it necessary to do a GO analysis on RNA seq data using those programs available such as BLAST2GO, Go seq ect.?
I greatly appreciate your inputs!
I'm sorry for not stating my question clearly. This is what I wanted to ask:
After analyzing RNA seq data, we assigned GO terms for deferentially expressed genes based on GO terms given by the reference assembly. We didn't do a separate GO analysis for RNA seq data. So what would you think about it? Is getting GO terms directly from the reference assembly is enough? OR do we have to do a separate GO analysis for the data?