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.
See: /Example/?/*RNA-seq analysis*/*tools*
http://cufflinks.cbcb.umd.edu/manual.html (search on page for
"gene_name" to see where can be used/output)
On 11/12/13 10:40 AM, Irene Bassano wrote:
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!
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