Running cufflinks for spliceR

Dear spliceR developer,

It's convenient that spliceR can take cuffdiff output from cufflinks tools.
But I wonder what's the recommended way to run cufflinks tools. I've read
the spliceR paper and bioConductor vignette, but could not find the related
information.

specifically:
1. is novel annotation necessary?
2. cufflinks can do novel annotation with or without reference genome,
which way would be recommended?
3. cuffdiff needs gtf input file. Will the canonical gtf annotations (e.g.
UCSC) be good enough? Or is the merged gtf (from multiple gtf files by
cufflinks/cuffmerge) better?
4. Should the gtf file used by readCufflinks() be the same as the one used
by cuffdiff?

Thanks

-Hanquan

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