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 UCSC.

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 France

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