This directory contains a dump of the UCSC genome annotation database for the Jan. 2010 (GGSC Nleu1.0/nomLeu1) assembly of the gibbon genome (nomLeu1, GGSC (NCBI project 13975, accession GCA_000146795.1)). 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 gibbon genome, see the project website: http://www.ncbi.nlm.nih.gov/bioproject/13975 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=nomLeu1 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/nomLeu1/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/nomLeu1/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/nomLeu1/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu1/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu1/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 nomLeu1 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql nomLeu1 --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 - nestedRepeats.sql 2011-11-22 15:47 1.9K nestedRepeats.txt.gz 2011-11-22 15:47 16M gold.sql 2011-11-22 15:47 1.6K gold.txt.gz 2011-11-22 15:47 3.2M chainGorGor3Link.sql 2011-11-22 15:47 1.5K chainGorGor3Link.txt.gz 2011-11-22 15:47 121M chainGorGor3.sql 2011-11-22 15:50 1.6K chainGorGor3.txt.gz 2011-11-22 15:50 15M chainHg19.sql 2011-11-22 15:50 1.6K gc5BaseBw.sql 2011-11-22 15:50 1.2K gc5BaseBw.txt.gz 2011-11-22 15:50 63 chainHg19.txt.gz 2011-11-22 15:50 16M simpleRepeat.sql 2011-11-22 15:51 1.9K simpleRepeat.txt.gz 2011-11-22 15:51 22M chromInfo.sql 2011-11-22 15:52 1.3K chromInfo.txt.gz 2011-11-22 15:52 90K netHg19.sql 2011-11-22 15:52 2.0K netHg19.txt.gz 2011-11-22 15:52 16M history.sql 2011-11-22 15:53 1.5K history.txt.gz 2011-11-22 15:53 433 rmsk.sql 2011-11-22 15:53 1.8K rmsk.txt.gz 2011-11-22 15:53 128M gap.sql 2011-11-22 15:54 1.5K gap.txt.gz 2011-11-22 15:54 2.3M netGorGor3.sql 2011-11-22 15:54 2.0K netGorGor3.txt.gz 2011-11-22 15:54 20M chainHg19Link.sql 2011-11-22 15:54 1.5K chainHg19Link.txt.gz 2011-11-22 15:55 136M tRNAs.sql 2012-04-16 03:21 1.7K tRNAs.txt.gz 2012-04-16 03:21 10K netMm10.sql 2012-10-21 03:38 2.1K netMm10.txt.gz 2012-10-21 03:39 70M chainMm10Link.sql 2012-10-21 03:39 1.5K chainMm10Link.txt.gz 2012-10-21 03:39 464M chainMm10.sql 2012-10-21 03:41 1.7K chainMm10.txt.gz 2012-10-21 03:41 57M grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 augustusGene.sql 2015-07-26 16:56 1.9K augustusGene.txt.gz 2015-07-26 16:56 2.1M microsat.sql 2015-08-23 22:14 1.5K microsat.txt.gz 2015-08-23 22:14 320K xenoMrna.sql 2016-02-21 20:37 2.1K xenoMrna.txt.gz 2016-02-21 20:37 301M chromAlias.sql 2016-09-15 18:00 1.4K chromAlias.txt.gz 2016-09-15 18:00 91K ensPep.sql 2018-02-04 08:24 1.3K ensPep.txt.gz 2018-02-04 08:24 6.0M ensemblSource.sql 2018-02-04 08:24 1.4K ensemblSource.txt.gz 2018-02-04 08:24 85K ensGtp.sql 2018-02-04 08:25 1.4K ensGtp.txt.gz 2018-02-04 08:25 280K ensGene.sql 2018-02-04 08:25 1.9K ensemblToGeneName.sql 2018-02-04 08:25 1.4K ensemblToGeneName.txt.gz 2018-02-04 08:25 154K ensGene.txt.gz 2018-02-04 08:25 2.2M all_mrna.sql 2020-08-22 12:49 2.1K all_mrna.txt.gz 2020-08-22 12:49 8.4K mrnaOrientInfo.sql 2020-08-22 12:49 1.8K mrnaOrientInfo.txt.gz 2020-08-22 12:49 3.2K xenoRefGene.sql 2020-08-22 13:34 2.0K xenoRefGene.txt.gz 2020-08-22 13:34 33M xenoRefFlat.sql 2020-08-22 13:34 1.7K xenoRefFlat.txt.gz 2020-08-22 13:34 30M xenoRefSeqAli.sql 2020-08-22 13:34 2.1K xenoRefSeqAli.txt.gz 2020-08-22 13:34 32M gbLoaded.sql 2020-08-22 13:34 1.6K gbLoaded.txt.gz 2020-08-22 13:34 15K trackDb.sql 2023-03-28 13:51 2.1K trackDb.txt.gz 2023-03-28 13:51 18K hgFindSpec.sql 2023-03-28 13:51 1.8K hgFindSpec.txt.gz 2023-03-28 13:51 716 tableDescriptions.sql 2024-08-31 02:03 1.4K tableDescriptions.txt.gz 2024-08-31 02:03 5.2K tableList.sql 2024-09-01 03:29 1.6K tableList.txt.gz 2024-09-01 03:29 2.3K bigFiles.sql 2024-09-01 03:29 1.4K bigFiles.txt.gz 2024-09-01 03:29 68