This directory contains a dump of the UCSC genome annotation database for the Jun. 2017 (CHOK1S_HZDv1/criGriChoV2) assembly of the chinese hamster genome (criGriChoV2, Eagle Genomics Ltd) . The annotations were generated by UCSC and collaborators worldwide. For more information about this assembly, please note the NCBI resources: https://www.ncbi.nlm.nih.gov/genome/2791 https://www.ncbi.nlm.nih.gov/genome/assembly/1422381 https://www.ncbi.nlm.nih.gov/bioproject/PRJEB21211 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=criGriChoV2 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.soe.ucsc.edu, then go to the directory goldenPath/criGriChoV2/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.soe.ucsc.edu/goldenPath/criGriChoV2/database/ . For a single file, e.g. gc5Base.txt.gz rsync -avzP rsync://hgdownload.soe.ucsc.edu/goldenPath/criGriChoV2/database/gc5Base.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.soe.ucsc.edu/goldenPath/criGriChoV2/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.soe.ucsc.edu/goldenPath/criGriChoV2/database/gc5Base.txt.gz' -O gc5Base.txt.gz 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 criGriChoV2 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql criGriChoV2 --local-infile=1 -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;' ----------------------------------------------------------------------------- GenBank Data Usage The GenBank database is designed to provide and encourage access within the scientific community to the most up to date and comprehensive DNA sequence information. Therefore, NCBI places no restrictions on the use or distribution of the GenBank data. However, some submitters may claim patent, copyright, or other intellectual property rights in all or a portion of the data they have submitted. NCBI is not in a position to assess the validity of such claims, and therefore cannot provide comment or unrestricted permission concerning the use, copying, or distribution of the information contained in GenBank. ----------------------------------------------------------------------------- All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory - netMm10.sql 2019-06-05 10:21 2.1K netMm10.txt.gz 2019-06-05 10:21 80M all_est.sql 2019-06-05 10:21 2.1K all_est.txt.gz 2019-06-05 10:21 838 all_mrna.sql 2019-06-05 10:21 2.1K all_mrna.txt.gz 2019-06-05 10:21 2.8M refFlat.sql 2019-06-05 10:21 1.7K refFlat.txt.gz 2019-06-05 10:21 39K augustusGene.sql 2019-06-05 10:21 1.9K augustusGene.txt.gz 2019-06-05 10:21 2.3M gold.sql 2019-06-05 10:21 1.7K gold.txt.gz 2019-06-05 10:21 1.2M refGene.sql 2019-06-05 10:21 1.9K refGene.txt.gz 2019-06-05 10:21 43K chainHg38.sql 2019-06-05 10:21 1.7K chainHg38.txt.gz 2019-06-05 10:22 442M chainHg38Link.sql 2019-06-05 10:23 1.5K chainHg38Link.txt.gz 2019-06-05 10:25 1.4G chainMm10.sql 2019-06-05 10:30 1.7K grp.sql 2019-06-05 10:30 1.4K grp.txt.gz 2019-06-05 10:30 213 refSeqAli.sql 2019-06-05 10:30 2.1K refSeqAli.txt.gz 2019-06-05 10:30 43K chainMm10.txt.gz 2019-06-05 10:31 412M chainMm10Link.sql 2019-06-05 10:32 1.5K chainMm10Link.txt.gz 2019-06-05 10:35 1.8G chromAlias.sql 2019-06-05 10:41 1.4K chromAlias.txt.gz 2019-06-05 10:41 80K history.sql 2019-06-05 10:41 1.6K history.txt.gz 2019-06-05 10:41 823 rmsk.sql 2019-06-05 10:41 1.9K rmsk.txt.gz 2019-06-05 10:42 107M chromInfo.sql 2019-06-05 10:42 1.4K chromInfo.txt.gz 2019-06-05 10:42 33K cpgIslandExt.sql 2019-06-05 10:42 1.7K cpgIslandExt.txt.gz 2019-06-05 10:42 410K cpgIslandExtUnmasked.sql 2019-06-05 10:42 1.7K cpgIslandExtUnmasked.txt.gz 2019-06-05 10:42 420K gap.sql 2019-06-05 10:42 1.6K gap.txt.gz 2019-06-05 10:42 728K intronEst.sql 2019-06-05 10:42 2.1K intronEst.txt.gz 2019-06-05 10:42 560 cytoBandIdeo.sql 2019-06-05 10:42 1.5K cytoBandIdeo.txt.gz 2019-06-05 10:42 31K microsat.sql 2019-06-05 10:42 1.5K microsat.txt.gz 2019-06-05 10:42 2.3M simpleRepeat.sql 2019-06-05 10:42 1.9K simpleRepeat.txt.gz 2019-06-05 10:42 23M tandemDups.sql 2019-06-05 10:42 1.8K tandemDups.txt.gz 2019-06-05 10:42 9.6M mrnaOrientInfo.sql 2019-06-05 10:42 1.8K mrnaOrientInfo.txt.gz 2019-06-05 10:42 848K nestedRepeats.sql 2019-06-05 10:42 1.9K nestedRepeats.txt.gz 2019-06-05 10:42 8.9M estOrientInfo.sql 2019-06-05 10:42 1.8K estOrientInfo.txt.gz 2019-06-05 10:42 286 netHg38.sql 2019-06-05 10:42 2.1K netHg38.txt.gz 2019-06-05 10:42 54M gapOverlap.sql 2019-06-05 10:43 1.8K gapOverlap.txt.gz 2019-06-05 10:43 232K gc5BaseBw.sql 2019-06-05 10:43 1.3K gc5BaseBw.txt.gz 2019-06-05 10:43 70 genscan.sql 2019-06-05 10:43 1.7K genscan.txt.gz 2019-06-05 10:43 3.2M ucscToINSDC.sql 2019-06-05 10:43 1.4K ucscToINSDC.txt.gz 2019-06-05 10:43 50K ucscToRefSeq.sql 2019-06-05 10:43 1.4K ucscToRefSeq.txt.gz 2019-06-05 10:43 62 windowmaskerSdust.sql 2019-06-05 10:43 1.5K windowmaskerSdust.txt.gz 2019-06-05 10:43 123M xenoRefFlat.sql 2019-06-05 10:43 1.7K xenoRefFlat.txt.gz 2019-06-05 10:43 29M xenoRefGene.sql 2019-06-05 10:43 1.9K xenoRefGene.txt.gz 2019-06-05 10:43 32M xenoRefSeqAli.sql 2019-06-05 10:43 2.1K xenoRefSeqAli.txt.gz 2019-06-05 10:43 29M ensGene.sql 2021-05-25 14:27 1.9K ensGene.txt.gz 2021-05-25 14:27 2.3M ensGtp.sql 2021-05-25 14:27 1.4K ensGtp.txt.gz 2021-05-25 14:27 297K ensemblToGeneName.sql 2021-05-25 14:27 1.4K ensemblToGeneName.txt.gz 2021-05-25 14:27 167K ensemblSource.sql 2021-05-25 14:32 1.4K ensemblSource.txt.gz 2021-05-25 14:32 87K ensPep.sql 2021-05-25 14:32 1.3K ensPep.txt.gz 2021-05-25 14:32 6.6M trackDb.sql 2023-03-28 13:47 2.1K trackDb.txt.gz 2023-03-28 13:47 43K hgFindSpec.sql 2023-03-28 13:47 1.8K hgFindSpec.txt.gz 2023-03-28 13:47 873 tableDescriptions.sql 2024-11-02 02:04 1.5K tableDescriptions.txt.gz 2024-11-02 02:04 5.6K tableList.sql 2024-11-03 03:05 1.6K tableList.txt.gz 2024-11-03 03:05 2.7K bigFiles.sql 2024-11-03 03:05 1.4K bigFiles.txt.gz 2024-11-03 03:05 73