To Whom it May Concern:
My name is Nicole McDaniels. I am a Ph.D. candidate at Syracuse University. I am attempting to use RNAseq to look at changes in the transcriptome of zebrafish embryos upon morpholino injection. I have been using Galaxy Main to manage my data thus far. Recently, I completed the cufflinks/cuffcompare/cuffdiff analysis. I now have cuffdiff files in the tabular format. I would like to assess the gene ontologies of the differentially expressed transcripts, but I'm having trouble figuring out how to transfer over to GO Galaxy and then what exactly I should be doing in GO Galaxy.
Is there a different program or server that would be better/easier for the gene ontology analysis than GO Galaxy? I've also looked at the GOseq R package, but again I'm not sure about the tabular file format or how to change it to a more appropriate format. Any help you can give me with this would be greatly appreciated. I thank you in advance for your time.
All the best,
Department of Biology