To Whom It May Concern, As you can see below, I am attempting to create a mirror of your site using only the data for chr16. In the email that was sent to me by Jennifer Jackson, she said that:
Data from /gbdb are: snpSeqFile /gbdb/hg18/snp/snp130.fa I was just wondering where I could find the snp130.fa file for download. I was not able to find it via your website; am I supposed to use rsync to download this? Kyle Tretina Wheaton College ---------- Forwarded message ---------- From: Jennifer Jackson <[email protected]> Date: Wed, Jan 20, 2010 at 2:49 AM Subject: Re: [Genome] Mirror Site Question To: Kyle Tretina <[email protected]> Cc: UCSC <[email protected]>, Pattle Pun <[email protected]> Hello Kyle, To start with, here are the main links to the FAQs about mirrors: http://genome.ucsc.edu/admin/mirror.html http://genomewiki.ucsc.edu/index.php/Category:Mirror_Site_FAQ For a minimum install: http://genomewiki.ucsc.edu/index.php/Browser_Mirrors http://genomewiki.ucsc.edu/index.php/Browser_installation http://genomewiki.ucsc.edu/index.php/Presentations -> 2009, 4 October Genecats meeting, Hiram Clawson - building the kent source tree and a UCSC genome browser assembly For creating a chr13 only database: http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database (rsync the minimum install files for hg19 and prune to include only data for chr16). For loading only a subset of the snp130 data or your own SNP track: http://genomewiki.ucsc.edu/index.php/Adding_New_Tracks_to_a_browser_install ation -> See Also "For a generic discussion of how to load any type of track into your local browser mirror, refer to the document in the source tree src/product/README.trackDb and the discussion of how the trackDb entries function in src/hg/makeDb/trackDb/README" In hg19's dbSNP(130) track: Database tables are: snp130 snp130CodingDbSnp snp130ExceptionDesc snp130Exceptions snp130OrthoPt2Pa2Rm2 snp130Seq Data from /gbdb are: snpSeqFile /gbdb/hg18/snp/snp130.fa (note that there is no data in /gbdb/hg19 specific for this assembly, instead data from /gbdb/hg18 was used, since it was the same. In the UCSC trackDb, there is a pointer to the files in hg18. You can create a /gbdb/hg18 directory or move the data into the hg19 directory and adjust the trackDb.ra file before installing) Hopefully this addresses all of your questions, but please let us know if you need more help after reviewing the documentation. You also might be interested in the genome-mirror mailing list (the best place to send mirror-related questions): http://genome.ucsc.edu/contacts.html -> scroll to the section titled "Mirroring" to subscribe or review/search the archives. Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Kyle Tretina" <[email protected]> wrote: > From: "Kyle Tretina" <[email protected]> > To: "UCSC" <[email protected]>, "Pattle Pun" <[email protected]> > Sent: Tuesday, January 19, 2010 5:13:04 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] Mirror Site Question > > To whom it may concern, > > I am an intern at Wheaton College trying to create a mirror site > for the > UCSC genome browser so that I can attempt the automation of the > alignment of > SNP sequences in hg19 on chr16 only. I have a list of rs numbers to > accomplish this and would not like to have to do them all manually on > your > site. I have two questions concerning this: > > 1) In step 4, what is the minimal /gbdb file area needed if I am only > interested in hg19, chr16? The whole gbdb file area seems to be > terrabytes. > > 2) In step 5 I am supposed to create a gbdb data file area and a > database > table area. How do I determine what files are needed for the database > table > area? > > > > Kyle Tretina > Wheaton College > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
