Hi Jennifer, Thanks.
I see I wasn't totally clear. When I asked about SQL commands to assemble the information, what I was essentially looking for was something like the refGene.sql file (giving the commands for creating the table that I filled with the refGene.txt file). Is there a way to get a SNPs130.sql (or something like that) file? (Describe Table Schema gives a nice description of the schema, but doesn't list the sql commands one would execute to make the table in MySQL.) IOW, you very nicely pointed me right to where I could get the data I want. Now I'm hoping you can point me to a tool that will let me avoid the mindless and repetitive task of creating MySQL tables to hold the data (since I'm sure I can screw that up a couple of times on the way to getting it right). :-) Thank you, Greg ----- Original Message ----- From: "Jennifer Jackson" <[email protected]> To: "Gregory Dougherty" <[email protected]> Cc: [email protected] Sent: Wednesday, September 1, 2010 1:02:51 PM GMT -06:00 US/Canada Central Subject: Re: [Genome] Mappings of repeats to chromosome positions Hello Greg, There is a "RepeatMasker" track in most assemblies and some also have other variations. Read each track description to understand the contents. A link into the table browser that points to the primary table is also on the track description page. From there you have some options: 1) use the Table browser to extract data 2) ftp the database file from the Downloads server - http://hgdownload.cse.ucsc.edu/downloads.html - Common name - Annotation database - primary table name (.txt.gz) Help for #1 & #2: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download1 3) use the public mySQL server. We cannot help with the exact query for all cases, but a quick google search brings up quite a bit of online help for more complex operations. Just swap in our table names and "select * from <table name>;" to get the whole table or modify/restrict as needed. Help for #3: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29 4) also on the downloads server are sequence files with repeat masking in them. The READMEs in these locations have file descriptions and more ftp help: ftp the database file from the Downloads server - http://hgdownload.cse.ucsc.edu/downloads.html - Common name - Full data set - review README for available files If you need more pointers to help/faqs, please let us know which you cannot find using the top blue navigation bars into these areas. Please feel free to contact the mailing list support team again if you would like more assistance. Best! Jen UCSC Genome Browser Support On 9/1/10 9:13 AM, Gregory Dougherty wrote: > A hopefully not too stupid question: > > What DB files from hg18 would I use to get the locations of repeats in the > genome, and what SQL comamnds (if any) would I use to assemble that > information? > > TIA, > > Greg > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
