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  • LMM
    Junior Member
    • Jan 2017
    • 8
    #1

    TopHat/ Cufflinks & ...EdgeR?

    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
    Tags: None
  • shunyip
    Member
    • Oct 2013
    • 20
    #2
    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, 12:29 PM.

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