Hi, You need to supply a gene annotation file with cufflink to easily get the gene-id information. Without it, cufflinks simply tries its best to figure out what genes are present. The ensemble gtf file is quite a comprehensive one - there is a link to it on the cufflinks manual page.
Good luck! David On 28 Feb 2011, at 21:33, Ying Zhang wrote: > Dear Everyone: > > I have got one output file after I run Cufflink which contain gene expression > information. However, I found out for each gene_ID, it has the format like, > CUFF.1151175, do you have idea of how to find out the offical gene ID > correspond to this CUFF ID? Thank you very much! > > Best > > Ying Zhang, M.D., Ph.D. > Postdoctoral Associate > Department of Genetics, > Yale University School of Medicine > 300 Cedar Street,S320 > New Haven, CT 06519 > Tel: (203)737-2616 > Fax: (203)737-2286 > _______________________________________________ > The Galaxy User list should be used for the discussion > of Galaxy analysis and other features on the public > server at usegalaxy.org. For discussion of local Galaxy > instances and the Galaxy source code, please use the > Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other > Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ _______________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
