Hello Michael, The UCSC RefSeq Genes track's has the data: 1) a transcript accession, in column "name" 2) a gene symbol, in column "name2" but not from the Table Browser's GTF format output, as explained at: http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format Ensembl is another data source choice for full functionality, at it contains: transcript_id, gene_id, and gene_name. This help from the tool authors is also worth reviewing: http://cufflinks.cbcb.umd.edu/gff.html Note that specific questions about these tools can also be directed at: tophat.cufflinks@gmail.com Hopefully this helps, Jen Galaxy team On 10/26/11 9:24 AM, Michael Gooch wrote:

Regarding the GTF files for cuffllinks, how do I obtain one for all human mRNA that actualy contains gene names rather than accession numbers. I went to the UCSC table browser but their files contain accession numbers that I dont know how to decode en-masse. ___________________________________________________________ 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/

-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support