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  • vramnarine
    Junior Member
    • Apr 2014
    • 5
    #1

    Cuffcompare : Reference or Merged transcriptome

    Hi All ,

    I would like to run cuffcompare but confused about what reference to supply it?

    With my workflow I run cuffmerge (after cufflinks) WITH an annotated reference supplied, so when I run cuffcompare should I supply the reference annotation again (only) or the merged annotation (only) or both?

    From my understanding when you run cuffmerge with a reference annotation, supplying the reference in cuffcompare is not necessary, only the merged annotation is.

    Just looking for some confirmation with that!

    Thanks
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