Hello guys,
I went through the RNAseq workflow (I didn't do Cuffmerge) and from the 
Cuffdiff output gene and transcript differential expression testing I filtered 
some data. For example, for two samples I got about 400 gene and 900 transcript 
differential expressed with fold change >2. Since I am working with a fungus 
whose genome annotation is in a format (gff) not accepted by Cuffmerge or 
Cuffcompare in Galaxy (the accepted one is GTF2), the Cuffdiff output tells me 
only the position of relevant genes on the scaffolds.
Going to genome browser and see which gene is in that position is fine for few 
genes, but doing that for all 400 or 900 is something probably impossible.
Does anybody have a helpful suggestion on what I can do? It would be great if 
there was a program where based on the position of the genes on the scaffold 
(Cuffdiff output) I can get their information using the annotation file. I have 
also the gene annotation file in gene bank format (gbk) but I don't see a way 
to use it for what I need.

Giuseppe Ianiri, Ph.D.
Division of Cell Biology and Biophysics
School of Biological Sciences
5100 Rockhill Road
University of Missouri-Kansas City
Kansas City, MO 64110
Email: iani...@umkc.edu

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