if I am looking for DE between samples and ran cufflinks without
reference annotation, does it mean that when I ran cuffcompare and
cuffmerge I DOTN'T HAVE to select a refence annotation in the options?

Also,how are my cufflinks fected wheter i use the reference annotation
or not?In galaxy tracker, looks like there are alignments missing or
added compared to when i ran cufflinks with a reference annotation

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