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