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://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.cufflinks@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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