Question: tophat-cuffdiff or tophat-cufflinks-cuffmerge-cuffdiff?
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4.9 years ago by
biolab1.2k wrote:

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 • 1.6k views
ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by biolab1.2k

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 REPLYlink modified 11 months ago by RamRS30k • written 4.9 years ago by mikhail.shugay3.4k

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

ADD REPLYlink written 4.9 years ago by biolab1.2k
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