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,

Nicole McDaniels
Ph.D Candidate
Syracuse University
Department of Biology
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