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 ----------------------------------------------------------------------- This message and its attachments are strictly confidential. If you are not the intended recipient of this message, please immediately notify the sender and delete it. Since its integrity cannot be guaranteed, its content cannot involve the sender's responsibility. Any misuse, any disclosure or publication of its content, either whole or partial, is prohibited, exception made of formally approved use -----------------------------------------------------------------------