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 - chainMm10Link.txt.gz 2019-06-05 10:35 1.8G chainHg38Link.txt.gz 2019-06-05 10:25 1.4G chainHg38.txt.gz 2019-06-05 10:22 442M chainMm10.txt.gz 2019-06-05 10:31 412M windowmaskerSdust.txt.gz 2019-06-05 10:43 123M rmsk.txt.gz 2019-06-05 10:42 107M netMm10.txt.gz 2019-06-05 10:21 80M netHg38.txt.gz 2019-06-05 10:42 54M xenoRefGene.txt.gz 2019-06-05 10:43 32M xenoRefFlat.txt.gz 2019-06-05 10:43 29M xenoRefSeqAli.txt.gz 2019-06-05 10:43 29M simpleRepeat.txt.gz 2019-06-05 10:42 23M tandemDups.txt.gz 2019-06-05 10:42 9.6M nestedRepeats.txt.gz 2019-06-05 10:42 8.9M ensPep.txt.gz 2021-05-25 14:32 6.6M genscan.txt.gz 2019-06-05 10:43 3.2M all_mrna.txt.gz 2019-06-05 10:21 2.8M microsat.txt.gz 2019-06-05 10:42 2.3M ensGene.txt.gz 2021-05-25 14:27 2.3M augustusGene.txt.gz 2019-06-05 10:21 2.3M gold.txt.gz 2019-06-05 10:21 1.2M mrnaOrientInfo.txt.gz 2019-06-05 10:42 848K gap.txt.gz 2019-06-05 10:42 728K cpgIslandExtUnmasked.txt.gz 2019-06-05 10:42 420K cpgIslandExt.txt.gz 2019-06-05 10:42 410K ensGtp.txt.gz 2021-05-25 14:27 297K gapOverlap.txt.gz 2019-06-05 10:43 232K ensemblToGeneName.txt.gz 2021-05-25 14:27 167K ensemblSource.txt.gz 2021-05-25 14:32 87K chromAlias.txt.gz 2019-06-05 10:41 80K ucscToINSDC.txt.gz 2019-06-05 10:43 50K refSeqAli.txt.gz 2019-06-05 10:30 43K trackDb.txt.gz 2023-03-28 13:47 43K refGene.txt.gz 2019-06-05 10:21 43K refFlat.txt.gz 2019-06-05 10:21 39K chromInfo.txt.gz 2019-06-05 10:42 33K cytoBandIdeo.txt.gz 2019-06-05 10:42 31K tableDescriptions.txt.gz 2024-11-02 02:04 5.6K tableList.txt.gz 2024-11-03 03:05 2.7K xenoRefSeqAli.sql 2019-06-05 10:43 2.1K refSeqAli.sql 2019-06-05 10:30 2.1K intronEst.sql 2019-06-05 10:42 2.1K all_mrna.sql 2019-06-05 10:21 2.1K all_est.sql 2019-06-05 10:21 2.1K netMm10.sql 2019-06-05 10:21 2.1K netHg38.sql 2019-06-05 10:42 2.1K trackDb.sql 2023-03-28 13:47 2.1K ensGene.sql 2021-05-25 14:27 1.9K augustusGene.sql 2019-06-05 10:21 1.9K xenoRefGene.sql 2019-06-05 10:43 1.9K nestedRepeats.sql 2019-06-05 10:42 1.9K simpleRepeat.sql 2019-06-05 10:42 1.9K refGene.sql 2019-06-05 10:21 1.9K rmsk.sql 2019-06-05 10:41 1.9K tandemDups.sql 2019-06-05 10:42 1.8K gapOverlap.sql 2019-06-05 10:43 1.8K mrnaOrientInfo.sql 2019-06-05 10:42 1.8K estOrientInfo.sql 2019-06-05 10:42 1.8K hgFindSpec.sql 2023-03-28 13:47 1.8K xenoRefFlat.sql 2019-06-05 10:43 1.7K cpgIslandExtUnmasked.sql 2019-06-05 10:42 1.7K refFlat.sql 2019-06-05 10:21 1.7K chainMm10.sql 2019-06-05 10:30 1.7K chainHg38.sql 2019-06-05 10:21 1.7K cpgIslandExt.sql 2019-06-05 10:42 1.7K genscan.sql 2019-06-05 10:43 1.7K gold.sql 2019-06-05 10:21 1.7K gap.sql 2019-06-05 10:42 1.6K tableList.sql 2024-11-03 03:05 1.6K history.sql 2019-06-05 10:41 1.6K chainMm10Link.sql 2019-06-05 10:32 1.5K chainHg38Link.sql 2019-06-05 10:23 1.5K cytoBandIdeo.sql 2019-06-05 10:42 1.5K windowmaskerSdust.sql 2019-06-05 10:43 1.5K microsat.sql 2019-06-05 10:42 1.5K tableDescriptions.sql 2024-11-02 02:04 1.5K ensGtp.sql 2021-05-25 14:27 1.4K ucscToRefSeq.sql 2019-06-05 10:43 1.4K ucscToINSDC.sql 2019-06-05 10:43 1.4K chromAlias.sql 2019-06-05 10:41 1.4K ensemblToGeneName.sql 2021-05-25 14:27 1.4K bigFiles.sql 2024-11-03 03:05 1.4K chromInfo.sql 2019-06-05 10:42 1.4K ensemblSource.sql 2021-05-25 14:32 1.4K grp.sql 2019-06-05 10:30 1.4K ensPep.sql 2021-05-25 14:32 1.3K gc5BaseBw.sql 2019-06-05 10:43 1.3K hgFindSpec.txt.gz 2023-03-28 13:47 873 all_est.txt.gz 2019-06-05 10:21 838 history.txt.gz 2019-06-05 10:41 823 intronEst.txt.gz 2019-06-05 10:42 560 estOrientInfo.txt.gz 2019-06-05 10:42 286 grp.txt.gz 2019-06-05 10:30 213 bigFiles.txt.gz 2024-11-03 03:05 73 gc5BaseBw.txt.gz 2019-06-05 10:43 70 ucscToRefSeq.txt.gz 2019-06-05 10:43 62