> 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?
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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