Hello Irene,
These are RefSeq transcript identifiers. In some GTF file sources,
transcript_id is also assigned to the gene_id attribute in the 9th
field, which can cause confusion. Alternative GTF sources are Ensembl
and iGenomes. However, examining differential expression at the
transcript level may be best, as Leonor explained in response to your
other recent post:
http://lists.bx.psu.edu/pipermail/galaxy-user/2012-July/004953.html
Thanks,
Jen
Galaxy team
On 7/26/12 1:59 PM, i b wrote:
Dear all,
has anything like this happened to you?
I compared two samples with cuffdiff and when I look at the
differentially expressed genes values I have the same gene listed for
5 times with different values.
E.g.
sample1 sample2 gene
71.6837 9.76435 NM_005514
87.6456 27.3965 NM_005514
115.333 4.81687 NM_005514
38.1879 5.2753 NM_005514
69.4197 5.84387 NM_005514
112.964 3.89226 NM_005514
What does this mean? And how do I know which one represents the real
expression level for that gene for the two samples?
Thanks,
ib
___________________________________________________________
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/
--
Jennifer Jackson
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/
