Hello Matteo,

The UCSC Genes table knownCanonical is one source for gene names, but another choice would be the RefSeq Genes track's primary table "refGene". When extracting from the UCSC Table browser, use the output file type of "all fields from selected table". The gene name will be under a column labeled as "name2" (as defined in the extended genePred format at UCSC and which is not included in BED or GTF format output file types).

As the other users have pointed out, a valid GTF file format for the Cuff* programs to use is the goal. Currently, some manipulation of the available reference files from many of the common sources is necessary to get the formatting correct. The Galaxy team is aware of the issues with external files concerning format and is working on potential solutions.

Thank you for your patience while we work out the kinks with the newly added tool suite,


Galaxy team

On 1/24/11 7:02 AM, Jeremy Goecks wrote:
Hi Matteo and Vasu,

There are different ways to refer to genes. Names that start with NM_
are termed 'accession numbers,' and they are a valid way to refer to genes.

Matteo, what you may want is the canonical gene name (e.g. Xkr4). If so,
you'll want to use a gene annotation/reference file from UCSC; when you
are getting the file, you'll want to select the table with the word
'canonical' in it. E.g. for hg19/UCSC genes, there is a table called
knownCanonical that provides the canonical gene names.


On Jan 24, 2011, at 9:38 AM, vasu punj wrote:

This is a knwon issue of GTF file from Ensembl

--- On *Mon, 1/24/11, Matteo Bovolenta /<bvl...@unife.it
<mailto:bvl...@unife.it>>/* wrote:

    From: Matteo Bovolenta <bvl...@unife.it <mailto:bvl...@unife.it>>
    Subject: [galaxy-user] Gene Name in Cufflink/compare/diff
    To: galaxy-u...@bx.psu.edu <mailto:galaxy-u...@bx.psu.edu>
    Date: Monday, January 24, 2011, 5:05 AM

    Hi all,

    when I run a RNASeq analysis using tophat, cufflink, coffcompare and
    cuffdiff by aligning my data to the RefSeq genes I obtain tables from
    cufflink/compare/diff which does not include the gene name, but only
    the NM_.
    Does someone knows how I can obtain all the tables with the gene name?

    Thank you all very much for the support,

    Best Regards,


    Matteo Bovolenta, PhD
    Dipartimento di Medicina Sperimentale e Diagnostica
    Sezione di Genetica Medica
    Università di Ferrara
    Via Fossato di Mortara, 74
    44100 Ferrara
    tel +39 0532 974449(office)
    tel +39 0532 974502 (lab)
    fax +39 0532 236157
    email bvl...@unife.it
    http://www.bio-nmd.eu <http://www.bio-nmd.eu/>
    registered in ORPHANET
    http://www.orpha.net <http://www.orpha.net/>

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