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LMM 02-16-2017 10:50 AM

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)

shunyip 02-16-2017 11:26 AM

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.

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