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.

Thanks