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,