Hello, The transcript name when using RefSeq as a reference annotation is the "NM_" type of identifier. If you want to include a gene symbol, then the reference annotation should include the attribute "gene_name". The iGenomes GTF files are an example of datasets that include this attribute. http://wiki.galaxyproject.org/Support#Interpreting_scientific_results See: /Example/?/*RNA-seq analysis*/*tools* http://cufflinks.cbcb.umd.edu/faq.html#gtfs http://cufflinks.cbcb.umd.edu/igenomes.html http://cufflinks.cbcb.umd.edu/manual.html (search on page for "gene_name" to see where can be used/output) Best, Jen Galaxy team On 11/12/13 10:40 AM, Irene Bassano wrote:
Dear Jennifer, I am about to start a new analysis and learning from my old mistakes would like to ask just one question: I would like my Cufflinks and Cuffdiff results to give me the actual gene name or transcript name rather than "NM_......" like I had last time i run the job.
At which stage and which option do I have ti use to get the proper names?
Thanks a lot!
Irene
-- Jennifer Hillman-Jackson http://galaxyproject.org -- Jennifer Hillman-Jackson http://galaxyproject.org