This directory contains a dump of the UCSC genome annotation database for the Sep. 2009 (TWGS Meug_1.1/macEug2) assembly of the wallaby genome (macEug2, TWGS (NCBI Project ID: 12586, Accession: GCA_000004035.1)). The annotations were generated by UCSC and collaborators worldwide. This assembly was produced by the National Center for Biotechnology Information (NCBI). For more information on the wallaby genome, see the project website: http://www.ncbi.nlm.nih.gov/bioproject/12587 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=macEug2 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/macEug2/database/. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - 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/macEug2/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/macEug2/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/macEug2/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/macEug2/database/gc5BaseBw.txt.gz' -O gc5BaseBw.txt.gz Please note that some files contents, such as this example gc5BaseBw.txt.gz, will point to the data being hosted in another /gbdb/ location, which refers to ftp://hgdownload.cse.ucsc.edu/gbdb/ To uncompress the *.txt.gz files: gunzip <table>.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 macEug2 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql macEug2 --local-infile=1 -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;' All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory - gap.sql 2012-01-19 11:16 1.5K gap.txt.gz 2012-01-19 11:16 9.3M gc5BaseBw.sql 2012-01-19 11:20 1.2K gc5BaseBw.txt.gz 2012-01-19 11:20 63 windowmaskerSdust.sql 2012-01-19 11:20 1.4K windowmaskerSdust.txt.gz 2012-01-19 11:21 156M rmsk.sql 2012-01-19 11:22 1.8K rmsk.txt.gz 2012-01-19 11:22 142M chromInfo.sql 2012-01-19 11:24 1.3K chromInfo.txt.gz 2012-01-19 11:24 1.4M gold.sql 2012-01-19 11:24 1.6K gold.txt.gz 2012-01-19 11:24 18M history.sql 2012-01-19 11:25 1.5K history.txt.gz 2012-01-19 11:25 270 nestedRepeats.sql 2012-01-19 11:27 1.9K nestedRepeats.txt.gz 2012-01-19 11:27 12M simpleRepeat.sql 2012-01-19 11:27 1.9K simpleRepeat.txt.gz 2012-01-19 11:27 18M cytoBandIdeo.sql 2013-04-28 18:15 1.5K cytoBandIdeo.txt.gz 2013-04-28 18:15 1.4M ucscToINSDC.sql 2013-09-15 15:55 1.4K ucscToINSDC.txt.gz 2013-09-15 15:55 2.1M netMm10.sql 2013-10-27 17:12 2.1K netMm10.txt.gz 2013-10-27 17:12 12M chainMm10.sql 2013-10-27 17:12 1.7K chainMm10.txt.gz 2013-10-27 17:12 84M chainMm10Link.sql 2013-10-27 17:12 1.5K chainMm10Link.txt.gz 2013-10-27 17:12 315M genscan.sql 2013-12-10 01:59 1.7K genscan.txt.gz 2013-12-10 01:59 2.2M grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 augustusGene.sql 2015-07-26 16:14 1.9K augustusGene.txt.gz 2015-07-26 16:14 1.6M microsat.sql 2015-08-23 20:50 1.5K microsat.txt.gz 2015-08-23 20:50 700K xenoMrna.sql 2016-02-21 19:11 2.1K xenoMrna.txt.gz 2016-02-21 19:11 253M chromAlias.sql 2016-09-15 17:59 1.4K chromAlias.txt.gz 2016-09-15 17:59 2.4M estOrientInfo.sql 2017-05-14 07:20 1.8K estOrientInfo.txt.gz 2017-05-14 07:20 3.4M intronEst.sql 2017-05-14 07:20 2.1K intronEst.txt.gz 2017-05-14 07:20 5.4M all_est.sql 2017-05-14 07:20 2.1K all_est.txt.gz 2017-05-14 07:20 12M mrnaOrientInfo.sql 2017-11-05 08:25 1.8K mrnaOrientInfo.txt.gz 2017-11-05 08:25 5.8K all_mrna.sql 2017-11-05 08:25 2.1K all_mrna.txt.gz 2017-11-05 08:25 22K xenoRefGene.sql 2020-08-19 14:23 2.0K xenoRefGene.txt.gz 2020-08-19 14:23 29M xenoRefFlat.sql 2020-08-19 14:23 1.7K xenoRefFlat.txt.gz 2020-08-19 14:23 26M xenoRefSeqAli.sql 2020-08-19 14:23 2.1K xenoRefSeqAli.txt.gz 2020-08-19 14:23 30M gbLoaded.sql 2020-08-19 14:23 1.6K gbLoaded.txt.gz 2020-08-19 14:23 30K trackDb.sql 2023-03-28 13:50 2.1K trackDb.txt.gz 2023-03-28 13:50 32K hgFindSpec.sql 2023-03-28 13:50 1.8K hgFindSpec.txt.gz 2023-03-28 13:50 619 tableDescriptions.sql 2024-10-05 02:03 1.5K tableDescriptions.txt.gz 2024-10-05 02:03 4.9K tableList.sql 2024-10-06 03:35 1.6K tableList.txt.gz 2024-10-06 03:35 2.1K bigFiles.sql 2024-10-06 03:35 1.4K bigFiles.txt.gz 2024-10-06 03:35 68