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Old 01-14-2014, 01:23 AM   #3
Location: Berlin

Join Date: Oct 2010
Posts: 71

Try bedtools intersect with your Cufflinks GTF and the GTF you used as reference annotation to see if there is any known annotation in the regions identified by Cufflinks (which should not be the case).

FYI: -g means that Cufflinks will perform a RABT assembly of novel transcripts, in case you only want quantification of known genes use -G.
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