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Old 02-16-2017, 10:50 AM   #1
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Location: Athens, Ohio

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Default TopHat/ Cufflinks & ...EdgeR?

Can't seem to find a definite answer to this: Is EdgeR compatible with Cufflinks?
(Im new to this & help is appreciated)
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Old 02-16-2017, 11:26 AM   #2
Location: San Francisco South Bay Area

Join Date: Oct 2013
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edgeR works best with raw counts. You should use tools like featureCounts or HTSeq with it.

Also, please note that there are a lot of newer software tools. Maybe you should take a look at tools like STAR, HISAT, StringTie, Kallisto, etc. to replace TopHat and Cufflinks.

Last edited by shunyip; 02-16-2017 at 11:29 AM.
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