Hello,

On 6/17/13 12:24 PM, Hoang, Thanh wrote:
Hi Jen,
Thank you very much for your quick response.

I have just downloaded GTF file ( Mus musculus, UCSC, mm10) from iGenome. Correct me if I am wrong. I should start everything from the beginning again by uploading the GTF file to Galaxy via FTP uploading. Then, start mapping and assembly and analyzing the transcript using the GTF file this time : TopHat>> Cufflink>> Cuffmerge -Cuffdiff ???
Yes, if not mapped against mm10, you will need to start from that step and work forward.

Also, do you know any good software to assign genes into functional groups ( Gene ontology) ?
See the tool " Phenotype Association -> g:Profiler" for one option. The UCSC Table browser may also offer GO annotation in a mm10 track that you can intersect or join your results to. Biomart's Unigene annotation is another great resource.

Best,

Jen
Galaxy team

Thank you so much for your help
Thanh


On Mon, Jun 17, 2013 at 2:30 PM, Jennifer Jackson <j...@bx.psu.edu <mailto:j...@bx.psu.edu>> wrote:

    Hello Thanh,

    These attributes would come from the reference GTF or GFF3 file
    that you are using (not the reference genome). It looks like you
    are not using one, or that it did not cover this particular gene
    bound.

    The iGenomes GTF files are preferred as they contains all of the
    attributes that will both populate these sorts of values, but also
    allow the full compliment of statistics to be generated by the
    tool package. This is explained in the tool's manual:
    http://cufflinks.cbcb.umd.edu <http://cufflinks.cbcb.umd.edu/>
    http://wiki.galaxyproject.org/Support#Tools_on_the_Main_server

    That said, I don't think there is an iGenomes GTF for the
    reference genome you have selected. I am not aware of a liftOver
    file either (but I could be wrong, you can ask UCSC). You also
    could try posting a question to the tophat.cuffli...@gmail.com
    <mailto:tophat.cuffli...@gmail.com> google group to see what
    others are using/what is available right now.

    It may come down to choosing which is more important for your
    project - the most current genome or better annotation.

    Good luck!

    Jen
    Galaxy team


    On 6/17/13 11:13 AM, Hoang, Thanh wrote:
    Hi guys,
    I am trying to examine gene differential expression in my mouse
    samples using :
    Cufflink >> Cuffmerge>>Cuffdiff
    The output from Cuffdiff shows only gene id, but not gene name:
test_id gene_id gene locus sample_1 sample_2

    XLOC_000001         XLOC_000001     -         1:3200263-3200566     
Epithelium      Fiber

    Could anyone tell me how to make the gene name show up?
    I used Mus_musculus.GRCm38.71.dna.toplevel.fa  as the reference
    sequence (not GRCm38/mm10 from UCSC table broswer because i think
    this may be old version).
    I have been trying to find a solution online but still very confused
    Thanks so much
    Thanh



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Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

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