Many thanks, Jennifer. We downloaded hapmapAllelesSummary.txt. We just want to make sure the 6th column is for the conservation score, such as 0, 0, 65, 0, 4 in the first 5 rows of the hapmapAllelesSummary.txt. Please see attachments. Appreciate your kind help.
Warmest regard, Jirong -----Original Message----- From: Jennifer Jackson [mailto:[email protected]] Sent: Tuesday, February 17, 2009 5:40 PM To: Long, Jirong Cc: [email protected] Subject: Re: [Genome] conservate score for HapMap SNPs Hello, You can ftp the files from our downloads server or save the files from the Table Browser. For ftp, go to the main browser web site http://genome.ucsc.edu/ and click on "Downloads" in the left blue navigation bar. For the most recent data for human (hg18), click on Human, then click into the Annotation Database directory. Files named like hapmapSnps*.txt.gz (and maybe hapmapAlleles*.txt.gz) are the files related to the HapMap SNPs track. Instructions for ftp access: For saving from the Table browser, go to the main browser web site http://genome.ucsc.edu/ and click on "Table Browser" in the left blue navigation bar. Select the clade, genome, assembly for the latest human. Set group: Variation and Repeats and track: HapMap SNPs. The associated tables will be in the tables pull-down menu. Use the "View table schema" button to view table contents (maybe be a useful tool anyway, even if you use ftp). Make sure that region: genome and output format: all fields from selected tables. Name the output file and it will save to your computer. For more info about the track, go into the Human assembly browser and click on the track name for a full description of methods, sources, etc. Thanks! Jennifer Jackson UCSC Genome Bioinformatics Group Long, Jirong wrote: > Dear Sir/Madam, > > > > We are wondering whether you have a ftp address that we can use to > download the conservative score for each of the HapMap SNPs? Thanks. > > > > Best, > > > > Jirong > > > > ******************************************* > > Jirong Long, PhD > > Assistant Professor > > Vanderbilt Epidemiology Center > > Vanderbilt Ingram Cancer Center > > Eighth floor, Suite 800 > > 2525 West End Avenue > > Nashville, TN 37203-1738 > > Tel: 615-343-6741 > Fax: 615-322-0502 > > E-mail: [email protected] > > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome >
585 chr1 45161 45162 rs10399749 0 + C/T C none 4 NO C 114 114 C 88 88 C 88 88 C 112 112 T 10 T 60 585 chr1 45256 45257 rs2949420 0 + A/T T none 2 NO none 0 0 T 90 90 T 88 88 none 0 0 none 0 A 60 585 chr1 45412 45413 rs2949421 65 + A/T A T 1 NO none 0 0 none 0 0 none 0 0 T 114 118 none 0 T 60 585 chr1 46843 46844 rs2691310 0 + A/C C none 1 NO none 0 0 none 0 0 none 0 0 C 120 120 C 97 T 60 585 chr1 72433 72434 rs4030303 4 - C/T C T 4 NO C 120 120 C 89 90 C 88 88 C 120 120 C 63 C 60
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