tophat-cuffdiff or tophat-cufflinks-cuffmerge-cuffdiff?

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9.0 years ago

biolab ★ 1.4k

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.

cuffdiff cufflinks • 2.4k views

ADD COMMENT • link updated 2.4 years ago by Ram 44k • written 9.0 years ago by biolab ★ 1.4k

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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.

ADD REPLY • link updated 5.0 years ago by Ram 44k • written 9.0 years ago by mikhail.shugay 3.5k

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Hi, Mikhail.shugay, thank you for pointing that post to me. It's very helpful.

ADD REPLY • link 9.0 years ago by biolab ★ 1.4k

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