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Old 03-05-2013, 05:07 AM   #1
Location: Barcelona

Join Date: Feb 2013
Posts: 14
Default How cuffdiff works?

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?

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Old 03-05-2013, 07:35 AM   #2
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Location: Charlottesville, VA

Join Date: May 2011
Posts: 112

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