> One question related to this If I am intrested in annotated 
> genes/transcripts, what change I may have to make in command line while 
> runnig Cufflinks so that it will give both unknown as well as known 
> transcrpts and genes?
> Thanks

You probably want the -g/--GTF-guide parameter; from the Cufflinks 
documentation:

--
Tells Cufflinks to use the supplied reference annotation (GFF) to guide RABT 
assembly. Reference transcripts will be tiled with faux-reads to provide 
additional information in assembly. Output will include all reference 
transcripts as well as any novel genes and isoforms that are assembled.
--

This isn't currently implemented in Galaxy's Cufflinks but probably will be in 
the future. As always, community contributions are most welcome; if you've 
implemented something in your Cufflinks/compare/diff Galaxy wrappers that isn't 
available in the Galaxy repository, please submit them to the Community site: 
http://community.g2.bx.psu.edu/ or send them to us.

Best,
J.
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