Cuffcompare : Reference or Merged transcriptome

[vramnarine]

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