tophat-cuffdiff or tophat-cufflinks-cuffmerge-cuffdiff?
Hi everyone,
I am curious of the difference of the tophat-cufflinks-cuffmerge-cuffdiff and tophat-cuffdiff procedures. I am working on a species with quite well annotated genome. Is it right that these two procedures are very similar in my case? If I omit cufflinks and cuffmerge, will my result be affected? THANK YOU in advance for your comments or answers.
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Possible duplicate question Tuxedo Suite: When To Skip Cufflinks/Cuffmerge?. Cufflinks step is essential in case you want (and have sufficient coverage) to discover novel transcripts.
Hi, Mikhail.shugay, thank you for pointing that post to me. It's very helpful.