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 <[email protected]
<mailto:[email protected]>> 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 [email protected]
<mailto:[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
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Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
___________________________________________________________
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