Hello, Using a reference annotation combines what is known with what is novel in your experiment. The "Common uses" section of this web page explains this concept: http://cufflinks.cbcb.umd.edu/tutorial.html The UCSC Known Genes track incorporates all of RefSeq Genes with other sources, giving it an advantage. But it is also created at a particular time (updated recently, check UCSC for exact dates for any track's last update). Tracks from Genbank are updated daily, includes RefSeq Genes, giving it an different advantage as time passes. One or both tracks may or may not be available, depending on the target genome. Another choice are the iGenomes builds at the Cufflinks web site for UCSC. The iGenomes 'genes.gtf. files have specific attributes populated that activate the full functionality of Cufflinks and related tools. These are: gene_id, transcript_id, gene_name, p_id, and tss_id. For an example of how these are used, see Cuffdiff usage, as explained here http://cufflinks.cbcb.umd.edu/howitworks.html#hdif. The iGenomes data are a popular choice and were recently updated. http://cufflinks.cbcb.umd.edu/igenomes.html (scroll down) Note: mm9 'genes.gtf' is in Shared Data Libraries on Galaxy main. Others are welcome to add to the post to share other good sources for GTF datasets that include the attributes this tool package can utilize. Best, Jen Galaxy team On 7/16/12 8:33 AM, Irene Bassano wrote:

HI guys, how do we know when to select a refernce annotation when running cufflinks?And if yes, which one from UCSC should we chose: refgene or knowngenes?

Thanks, ib

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