TopHat/ Cufflinks & ...EdgeR?

[LMM]

Hello
Can't seem to find a definite answer to this: Is EdgeR compatible with Cufflinks?
(Im new to this & help is appreciated)
Cheers
Laura

[shunyip]

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.