Hello Jiang, Those files do not contain explicit 3' UTR coordinates, you will need to use the information in the file to infer the coordinates. For instructions on how to do this please see this previously answered mailing list question:
https://lists.soe.ucsc.edu/pipermail/genome/2009-February/018128.html Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu chunjiang he wrote: > Thanks Pauline, > I am sorry I can't find the file including the 3'UTR coordinates in > ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/ > I see the knownGene or RefGene files but I don't find the 3'utr > coordinates info there. > Can you guide me more? > Thanks very much. > > Jiang > On Tue, Jul 14, 2009 at 5:09 PM, Pauline Fujita <[email protected] > <mailto:[email protected]>> wrote: > > Hello Jiang, > > You can follow the analogous steps for mouse as outlined in this > previously answered mailing list question about coordinates for 3' > UTRs in human: > > https://lists.soe.ucsc.edu/pipermail/genome/2008-December/017718.html > > i.e. you will want to go to the mouse downloads page: > ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/ > > If you interested in the UCSC genes track in particular, you will > want the "knownGene*" files. > > Hopefully this information was helpful and answers your question. If > you have further questions or require clarification feel free to > contact the mailing list at [email protected] > <mailto:[email protected]>. > > Regards, > > Pauline Fujita > UCSC Genome Bioinformatics Group > http://genome.ucsc.edu <http://genome.ucsc.edu/> > > chunjiang he wrote: > > Hi all, > > I want to ask if there has a 3'UTR database in UCSC annotation > files. > Because I am looking for the genomic location of 3'UTR of all > mouse genes. > Or can you tell me another method to get the info. > Thanks. > > Jiang > _______________________________________________ > Genome maillist - [email protected] <mailto:[email protected]> > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
