Hello, I'm attaching previous correspondence below with the background for this question: I've been following a certain gen, Snhg12, in mouse mm9 for a while and am perplexed by how UCSC manages its tables. Initially I downloaded the refGene.sql and refGene.txt files from the mouse downloads page and copied them into my local MySQL version of UCSC (I have a couple tables stored locally for quick and easy access). This table (from about 2 years ago) doesn't contain the Snhg12 gene. I later came across the gene in the UCSC browser and noticed it was Refseq provisional status (light blue). I assumed that's why I don't see it in my local refGene table, but I asked about it below to see if I might find it somewhere. Upon receiving the answer I tried Vanessa's suggestion (below) which worked. The Snhg12 gene was in the results with provisional status. I recently retried Vanessa's suggestion and noticed that the status has been updated to "Validated" in both the table browser and the genome browser. So I have three different results for Snhg12 depending on when and how I access the data, yet all of them belong to the same 'mm9' version! Isn't this a litle problematic? Is there a reason why these changes aren't saved up for 'mm10'? The implications for my research and perhaps others' as well is that when we say 'mm9' it isn't the same thing and something that was 'intergenic' one day is now an 'exon' for example. Am I missing something here? I'm just trying to do as precise research as possible so as not to mislead... Thanks, Ilana **************************************************************** Dear Ilana,
Please see this previously answered mailing list question that tells how to get the status data using the table browser: https://lists.soe.ucsc.edu/pipermail/genome/2008-January/015354.html The data that you are looking for is located in this table: "refSeqStatus" in the mm9 database. Hope this helps! If you have further questions, please contact the mailing list ([email protected]). Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Ilana Livyatan" <[email protected]> To: [email protected] Sent: Thursday, February 24, 2011 1:56:58 AM Subject: [Genome] Getting Provisional Refseq genes Hi, I've downloaded the mysql versions of refgene mm9 and have a local database going. I noticed that this version doesn't include the provisional annotations. They do appear in the genome browser as a track with lighter blue color. How do I access and download these provisional Refseq annotations? I don't want all the UCSC known genes which seem to include these provisionals but a way to identify them as a separate group. Thanks for the help! Ilana Livyatan Dr. Eran Meshorer's Lab Department of Genetics Room 2-544, Givat Ram The Hebrew University of Jerusalem Jerusalem, 91904 ISRAEL Tel: 972-2-6585143 Fax: 972-2-6586975 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
