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Old 12-17-2013, 01:45 AM   #2
Stefano Manzini
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Location: Milan

Join Date: Dec 2013
Posts: 3
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Hello sohnic,

I have no answer to your question, but I would like to ask you one because you're posting about the very same issue I am wondering about.

Can you just give me some hints about the difference of using (or not) a local reference to run cufflinks?
I would like to understand what does cufflinks use to assembly the information contained in target.bam file when you don't provide it a local reference. Further, I'd also like to know whether using it will make cufflinks name the transcripts with the gene names instead of CUFF.65279 and the like.

Thank you for your help.
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