I generally take the GTF file to UCSC genome browser. If you are visualizing Bam file after alignment. I found IGV convinenet, though you may be able to visualize in Galaxy. Vasu --- On Fri, 5/6/11, puvan001@umn.edu <puvan001@umn.edu> wrote: From: puvan001@umn.edu <puvan001@umn.edu> Subject: Re: [galaxy-user] RNA seq analysis To: "David Matthews" <D.A.Matthews@bristol.ac.uk> Cc: galaxy-user@lists.bx.psu.edu Date: Friday, May 6, 2011, 7:30 PM Hello I was able to run RNA seq data against a custom build genome. How can I visualize the results. I tried via trackster and unfortunately I couldn't. Can you help me? Thanks Sumathy ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/