Hi all
From what I see in this forum, the common pipeline for Cufflinks is to run it without a reference annotation and supply the annotation only to cuffcompare.
If I run cufflinks with annotation, it will not build novel transcripts, but are there any additional considerations?
i.e. If I don't care about novel transcripts, is it better/recommended for me to run cufflinks with annotation?
thanks in advance,
Reut
From what I see in this forum, the common pipeline for Cufflinks is to run it without a reference annotation and supply the annotation only to cuffcompare.
If I run cufflinks with annotation, it will not build novel transcripts, but are there any additional considerations?
i.e. If I don't care about novel transcripts, is it better/recommended for me to run cufflinks with annotation?
thanks in advance,
Reut
Comment