> 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 

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.

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