How cuffdiff works?

[babi2305]

Greetings everyone!

I am stuck with cuffdiff output. Can anyone please give me an idea about how cuffdiff works? I am more interested in finding novel genes/isoforms. I gave the combined.gtf (from cuffcompare) file & sam files of both my samples to cuffdiff as input. I want to know, which genes/isoforms are the one that are novel with respect to the other sample. Does cuffdiff returns the novel ones also or just the differently expressed known genes between two samples?

I ran cufflinks with -g option to get the novel transcripts. Somebody please tell me how cuffdiff works?

Thanks

[turnersd]

Perhaps not the most accessible description, but this is from the official documentation:

http://cufflinks.cbcb.umd.edu/howitworks.html#hdif