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seq_newbie 07-15-2011 07:25 AM

cufflinks query

I have used different cufflinks transcripts.gtf files (from different lanes of multiple flow cells) and am using a software that produces splice graphs (gff files) on these files. My output has the same gene ID (e.g. CUFF.59062.gff) mapped to several different chromosomes).

I want to know is it possible for cufflinks to isolate it's gene ID's to a run and use the same ID on a different gene for a subsequent run? Or might it be an issue with the software I'm using to generate the graph files?



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