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