Dear all,

I am analyzing RNA-Seq data and I would like to compare my cufflinks 
transcripts to an annotated transcriptome.

Following the steps described in the paper by Trapnell et al Nature 
Biotechnology, 2010, I have read that authors ran cuffcompare against a 
combined annotated transcriptomes of the UCSC known genes, Ensembl and Vega.
 My question is how do you build such a combined file? For the moment, I was 
able just to compare my data with an annotated transcriptome obtained only by 

I thank you for your help

Best regards

Davide Degli Esposti
Davide Degli Esposti, PhD
Epigenetic (EGE) Group
International Agency for Research on Cancer
Tel. +33 4 72738036
Fax. +33 4 72738322
150, cours Albert Thomas
69372 Lyon Cedex 08

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