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.

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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;'

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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 - ucscToRefSeq.txt.gz 2019-06-05 10:43 62 gc5BaseBw.txt.gz 2019-06-05 10:43 70 bigFiles.txt.gz 2024-10-13 03:06 73 grp.txt.gz 2019-06-05 10:30 213 estOrientInfo.txt.gz 2019-06-05 10:42 286 intronEst.txt.gz 2019-06-05 10:42 560 history.txt.gz 2019-06-05 10:41 823 all_est.txt.gz 2019-06-05 10:21 838 hgFindSpec.txt.gz 2023-03-28 13:47 873 gc5BaseBw.sql 2019-06-05 10:43 1.3K ensPep.sql 2021-05-25 14:32 1.3K grp.sql 2019-06-05 10:30 1.4K ensemblSource.sql 2021-05-25 14:32 1.4K chromInfo.sql 2019-06-05 10:42 1.4K bigFiles.sql 2024-10-13 03:06 1.4K ensemblToGeneName.sql 2021-05-25 14:27 1.4K chromAlias.sql 2019-06-05 10:41 1.4K ucscToINSDC.sql 2019-06-05 10:43 1.4K ucscToRefSeq.sql 2019-06-05 10:43 1.4K ensGtp.sql 2021-05-25 14:27 1.4K tableDescriptions.sql 2024-10-12 02:04 1.5K microsat.sql 2019-06-05 10:42 1.5K windowmaskerSdust.sql 2019-06-05 10:43 1.5K cytoBandIdeo.sql 2019-06-05 10:42 1.5K chainHg38Link.sql 2019-06-05 10:23 1.5K chainMm10Link.sql 2019-06-05 10:32 1.5K history.sql 2019-06-05 10:41 1.6K tableList.sql 2024-10-13 03:06 1.6K gap.sql 2019-06-05 10:42 1.6K gold.sql 2019-06-05 10:21 1.7K genscan.sql 2019-06-05 10:43 1.7K cpgIslandExt.sql 2019-06-05 10:42 1.7K chainHg38.sql 2019-06-05 10:21 1.7K chainMm10.sql 2019-06-05 10:30 1.7K refFlat.sql 2019-06-05 10:21 1.7K cpgIslandExtUnmasked.sql 2019-06-05 10:42 1.7K xenoRefFlat.sql 2019-06-05 10:43 1.7K hgFindSpec.sql 2023-03-28 13:47 1.8K estOrientInfo.sql 2019-06-05 10:42 1.8K mrnaOrientInfo.sql 2019-06-05 10:42 1.8K gapOverlap.sql 2019-06-05 10:43 1.8K tandemDups.sql 2019-06-05 10:42 1.8K rmsk.sql 2019-06-05 10:41 1.9K refGene.sql 2019-06-05 10:21 1.9K simpleRepeat.sql 2019-06-05 10:42 1.9K nestedRepeats.sql 2019-06-05 10:42 1.9K xenoRefGene.sql 2019-06-05 10:43 1.9K augustusGene.sql 2019-06-05 10:21 1.9K ensGene.sql 2021-05-25 14:27 1.9K trackDb.sql 2023-03-28 13:47 2.1K netHg38.sql 2019-06-05 10:42 2.1K netMm10.sql 2019-06-05 10:21 2.1K all_est.sql 2019-06-05 10:21 2.1K all_mrna.sql 2019-06-05 10:21 2.1K intronEst.sql 2019-06-05 10:42 2.1K refSeqAli.sql 2019-06-05 10:30 2.1K xenoRefSeqAli.sql 2019-06-05 10:43 2.1K tableList.txt.gz 2024-10-13 03:06 2.7K tableDescriptions.txt.gz 2024-10-12 02:04 5.6K cytoBandIdeo.txt.gz 2019-06-05 10:42 31K chromInfo.txt.gz 2019-06-05 10:42 33K refFlat.txt.gz 2019-06-05 10:21 39K refGene.txt.gz 2019-06-05 10:21 43K trackDb.txt.gz 2023-03-28 13:47 43K refSeqAli.txt.gz 2019-06-05 10:30 43K ucscToINSDC.txt.gz 2019-06-05 10:43 50K chromAlias.txt.gz 2019-06-05 10:41 80K ensemblSource.txt.gz 2021-05-25 14:32 87K ensemblToGeneName.txt.gz 2021-05-25 14:27 167K gapOverlap.txt.gz 2019-06-05 10:43 232K ensGtp.txt.gz 2021-05-25 14:27 297K cpgIslandExt.txt.gz 2019-06-05 10:42 410K cpgIslandExtUnmasked.txt.gz 2019-06-05 10:42 420K gap.txt.gz 2019-06-05 10:42 728K mrnaOrientInfo.txt.gz 2019-06-05 10:42 848K gold.txt.gz 2019-06-05 10:21 1.2M augustusGene.txt.gz 2019-06-05 10:21 2.3M ensGene.txt.gz 2021-05-25 14:27 2.3M microsat.txt.gz 2019-06-05 10:42 2.3M all_mrna.txt.gz 2019-06-05 10:21 2.8M genscan.txt.gz 2019-06-05 10:43 3.2M ensPep.txt.gz 2021-05-25 14:32 6.6M nestedRepeats.txt.gz 2019-06-05 10:42 8.9M tandemDups.txt.gz 2019-06-05 10:42 9.6M simpleRepeat.txt.gz 2019-06-05 10:42 23M xenoRefSeqAli.txt.gz 2019-06-05 10:43 29M xenoRefFlat.txt.gz 2019-06-05 10:43 29M xenoRefGene.txt.gz 2019-06-05 10:43 32M netHg38.txt.gz 2019-06-05 10:42 54M netMm10.txt.gz 2019-06-05 10:21 80M rmsk.txt.gz 2019-06-05 10:42 107M windowmaskerSdust.txt.gz 2019-06-05 10:43 123M chainMm10.txt.gz 2019-06-05 10:31 412M chainHg38.txt.gz 2019-06-05 10:22 442M chainHg38Link.txt.gz 2019-06-05 10:25 1.4G chainMm10Link.txt.gz 2019-06-05 10:35 1.8G