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 [email protected] 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
___________________________________________________________
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
___________________________________________________________
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
