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

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