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