Hello Kayla, Can you explain exactly what a "GenBank RNA" is? Is this just defined as a non-RefSeq, non-EST, non-protein sequence? Investigator submitted, non-large scale cDNA? Thanks, Katheleen
Katheleen Gardiner, PhD Professor Department of Pediatrics University of Colorado Denver Mail Stop 8313, 12800 E 19th Avenue PO Box 6511 Aurora CO 80045 tel. 303-724-0572 fax. 303-724-3838 [email protected] -----Original Message----- From: Kayla Smith [mailto:[email protected]] Sent: Wednesday, February 18, 2009 3:03 PM To: Huang, Xiaolu Cc: [email protected]; Gardiner, Katheleen Subject: Re: [Genome] some questions about the ucsc genes Hello Xiaolu, The link you gave us is actually for a mirror of our website, but I can still help you out. To download UCSC Genes, you can either go here and search for knownGenes.txt.gz: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ Or use the Table Browser: http://genome.ucsc.edu/cgi-bin/hgTables In the "Methods" section of the UCSC Genes details page, you will see: The UCSC Genes are built using a multi-step pipeline: 1. RefSeq and GenBank RNAs are aligned to the genome with BLAT, keeping only the best alignments for each RNA and discarding alignments of less than 98% identity. I hope this information is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group Huang, Xiaolu wrote: > Dear bioinformaticians at UCSC genome browser, > > I highly appreciate for all the help you have provided us. Here, I have some > more questions. Could you let me know how to download all UCSC predicted > genes. Also at your "UCSC gene track setting" page > http://genome-mirror.duhs.duke.edu/cgi-bin/hgTrackUi?hgsid=937667&c=chr3&g=knownGene, > you have mentioned the use of GeneBank RNA. Could you let me know what is > the criteria for selecting the GeneBank RNA? > > Thanks! > > Xiaolu > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
