This directory contains a dump of the UCSC genome annotation database for
the Dec. 2011 (v3.0.1/chrPic1) assembly of the painted turtle genome
(chrPic1, International Painted Turtle Genome Sequencing Consortium (GCA_000241765.1)).
The annotations were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
http://www.ncbi.nlm.nih.gov/genome/12107
http://www.ncbi.nlm.nih.gov/genome/assembly/326468
http://www.ncbi.nlm.nih.gov/bioproject/78657
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=chrPic1
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.cse.ucsc.edu, then go to
the directory goldenPath/chrPic1/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/chrPic1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/chrPic1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/chrPic1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/chrPic1/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 chrPic1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql chrPic1 --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.
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Name Last modified Size Description
Parent Directory -
simpleRepeat.sql 2012-06-08 16:43 1.9K
simpleRepeat.txt.gz 2012-06-08 16:43 8.9M
cpgIslandExt.sql 2012-06-08 16:44 1.6K
cpgIslandExt.txt.gz 2012-06-08 16:44 663K
rmsk.sql 2012-06-11 04:41 1.8K
rmsk.txt.gz 2012-06-11 04:42 17M
chainMm10Link.sql 2012-06-11 05:05 1.5K
chainMm10Link.txt.gz 2012-06-11 05:09 178M
chromInfo.sql 2012-06-11 05:23 1.3K
chromInfo.txt.gz 2012-06-11 05:23 277K
gap.sql 2012-06-11 05:23 1.5K
gap.txt.gz 2012-06-11 05:23 5.5M
history.sql 2012-06-11 05:26 1.5K
history.txt.gz 2012-06-11 05:26 401
genscan.sql 2012-06-11 05:41 1.6K
genscan.txt.gz 2012-06-11 05:41 2.5M
gc5BaseBw.sql 2012-06-11 05:41 1.2K
gc5BaseBw.txt.gz 2012-06-11 05:41 63
gold.sql 2012-06-11 05:41 1.6K
gold.txt.gz 2012-06-11 05:42 7.9M
genscanSubopt.sql 2012-06-11 05:58 1.5K
genscanSubopt.txt.gz 2012-06-11 05:59 5.7M
chainMm10.sql 2012-06-11 05:59 1.6K
chainMm10.txt.gz 2012-06-11 05:59 28M
nestedRepeats.sql 2012-06-11 06:01 1.9K
nestedRepeats.txt.gz 2012-06-11 06:01 554K
netMm10.sql 2012-06-11 06:01 2.0K
netMm10.txt.gz 2012-06-11 06:01 11M
windowmaskerSdust.sql 2012-06-11 06:02 1.4K
windowmaskerSdust.txt.gz 2012-06-11 06:04 107M
cytoBandIdeo.sql 2013-04-28 12:12 1.5K
cytoBandIdeo.txt.gz 2013-04-28 12:12 285K
ucscToINSDC.sql 2013-09-15 10:23 1.4K
ucscToINSDC.txt.gz 2013-09-15 10:23 480K
grp.sql 2014-03-02 03:40 1.3K
grp.txt.gz 2014-03-02 03:40 208
cpgIslandExtUnmasked.sql 2014-06-01 10:19 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 10:19 2.0M
augustusGene.sql 2015-07-26 11:38 1.9K
augustusGene.txt.gz 2015-07-26 11:38 2.2M
microsat.sql 2015-08-23 12:36 1.5K
microsat.txt.gz 2015-08-23 12:36 255K
all_mrna.sql 2020-05-06 04:40 2.1K
all_mrna.txt.gz 2020-05-06 04:40 4.3K
mrnaOrientInfo.sql 2020-05-06 04:41 1.8K
mrnaOrientInfo.txt.gz 2020-05-06 04:41 1.1K
xenoMrna.sql 2020-08-18 17:59 2.1K
xenoMrna.txt.gz 2020-08-18 17:59 296M
xenoRefGene.sql 2020-08-18 18:23 2.0K
xenoRefGene.txt.gz 2020-08-18 18:23 34M
xenoRefFlat.sql 2020-08-18 18:23 1.7K
xenoRefFlat.txt.gz 2020-08-18 18:23 30M
xenoRefSeqAli.sql 2020-08-18 18:23 2.1K
xenoRefSeqAli.txt.gz 2020-08-18 18:23 33M
gbLoaded.sql 2020-08-18 18:39 1.6K
gbLoaded.txt.gz 2020-08-18 18:39 34K
trackDb_pushedout.sql 2021-08-02 14:27 2.1K
trackDb_pushedout.txt.gz 2021-08-02 14:27 24K
hgFindSpec_pushedout.sql 2021-08-02 14:27 1.8K
hgFindSpec_pushedout.txt.gz 2021-08-02 14:27 606
trackDb.sql 2023-03-28 13:47 2.1K
trackDb.txt.gz 2023-03-28 13:47 26K
hgFindSpec.sql 2023-03-28 13:47 1.8K
hgFindSpec.txt.gz 2023-03-28 13:47 646
tableDescriptions.sql 2024-04-20 02:03 1.5K
tableDescriptions.txt.gz 2024-04-20 02:03 5.0K
tableList.sql 2024-04-21 03:37 1.6K
tableList.txt.gz 2024-04-21 03:37 2.2K
bigFiles.sql 2024-04-21 03:37 1.4K
bigFiles.txt.gz 2024-04-21 03:37 68