Hello Galaxy community, 

I recently entered in RNA-Seq world, I’m a second year PhD. 

We have recently sequenced a bacterial transcriptome. I would like to create the GTF or GFF3 file from the bacterial genome in order to add it to Cufflinks. The draft genome is still unpublished. We have run the PGAAP [URL="http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html"]http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html[/URL] pipeline to annotate it, but PGAAP do not gives GTF or GFF3 file. Instead, PGAAP gives you GenBank File. If someone could advise me how to do it I will be very grateful. Maybe Artemis can do it.

Last, say that I'm a biologist, so I need GUI to work, no programming experience, sorry.

Thank you very much, Bernardo