This directory contains a dump of the UCSC genome annotation database for the Mar. 2012 (RGSC 5.0/rn5) assembly of the rat genome (rn5, RGSC Rnor_5.0 (GCA_000001895.3)) from the Rat Genome Sequencing Consortium. The annotations were generated by UCSC and collaborators worldwide. For more information about this assembly, please note the NCBI resources: http://www.ncbi.nlm.nih.gov/genome/73 http://www.ncbi.nlm.nih.gov/genome/assembly/382928 http://www.ncbi.nlm.nih.gov/bioproject/16219 Files included in this directory (updated nightly): - *.sql files: the MySQL commands used to create the tables - *.txt.gz files: the database tables in a tab-delimited format compressed with gzip. To see descriptions of the tables underlying Genome Browser annotation tracks, select the table in the Table Browser: http://genome.ucsc.edu/cgi-bin/hgTables?db=rn5 and click the "describe table schema" button. There is also a "view table schema" link on the configuration page for each track. --------------------------------------------------------------- If you plan to download a large file or multiple files from this directory, we recommend you use ftp rather than downloading the files via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to the directory goldenPath/rn5/database/. To download multiple files, use the "mget" command: mget ... - or - mget -a (to download all the files in the directory) Alternate methods to ftp access. Using an rsync command to download the entire directory: rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/rn5/database/ . For a single file, e.g. gc5Base.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/rn5/database/gc5Base.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/rn5/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/rn5/database/gc5Base.txt.gz' -O gc5Base.txt.gz To uncompress the *.txt.gz files: gunzip .txt.gz The tables can be loaded directly from the .txt.gz compressed file. It is not necessary to uncompress them to load into a database, as shown in the example below. To load one of the tables directly into your local mirror database, for example the table chromInfo: ## create table from the sql definition $ hgsql rn5 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql rn5 --local-infile=1 -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;' ------------------------------------------------------------------ These data are made available before scientific publication with the following understanding: 1. The data may be freely downloaded, used in analyses, and repackaged in databases. 2. Users are free to use the data in scientific papers analyzing particular genes and regions if the providers of this data (the Rat Genome Sequencing Consortium) are properly acknowledged. 3. The Centers producing the data reserve the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). 4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects (see http://www.wellcome.ac.uk/en/1/awtpubrepdat.html) and the resulting NHGRI policy statement (http://www.genome.gov/page.cfm?pageID=10506537). 5. Any redistribution of the data should carry this notice.