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.cuffli...@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.
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