This directory contains a dump of the UCSC genome annotation database for
the July 2005 (Broad/echTel1) assembly of the tenrec genome (echTel1, Broad July 2005).
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/234
http://www.ncbi.nlm.nih.gov/genome/assembly/229058
http://www.ncbi.nlm.nih.gov/bioproject/12590
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=echTel1
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/echTel1/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/echTel1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/echTel1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/echTel1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/echTel1/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 echTel1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql echTel1 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
The Tenrec sequence is made freely available before scientific publication
with the following understanding:
1. The data may be freely downloaded, used in analyses, and repackaged in
databases.
2. Users are free to use the data in scientific papers analyzing particular
genes and regions if the provider of these data (The Broad Institute) is
properly acknowledged.
3. The center producing the data reserves the right to publish the initial
large-scale analyses of the data set, including large-scale identification
of regions of evolutionary conservation and large-scale genomic assembly.
Large-scale refers to regions with size on the order of a chromosome (that
is, 30 Mb or more).
4. Any redistribution of the data should carry this notice. 1. The data may
be freely downloaded, used in analyses, and repackaged in databases.
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
chainHg19Link.txt.gz 2012-07-29 11:20 646M
chainMm10Link.txt.gz 2012-06-28 23:10 299M
chainHg19.txt.gz 2012-07-29 11:19 195M
windowmaskerSdust.txt.gz 2012-06-28 23:12 125M
quality.txt.gz 2012-06-28 23:07 73M
rmsk.txt.gz 2012-06-28 23:08 69M
chainMm10.txt.gz 2012-06-28 23:14 67M
netHg19.txt.gz 2012-07-29 11:23 47M
xenoRefSeqAli.txt.gz 2020-08-21 15:32 43M
xenoRefGene.txt.gz 2020-08-21 15:32 38M
xenoRefFlat.txt.gz 2020-08-21 15:32 34M
netMm10.txt.gz 2012-06-28 23:09 27M
gold.txt.gz 2012-06-28 23:09 11M
genscanSubopt.txt.gz 2012-06-28 23:06 9.3M
simpleRepeat.txt.gz 2012-06-28 23:06 6.2M
gap.txt.gz 2012-06-28 23:19 5.4M
nestedRepeats.txt.gz 2012-06-28 23:07 5.2M
genscan.txt.gz 2012-06-28 23:19 5.1M
ensPep.txt.gz 2019-02-10 03:41 4.4M
ensGene.txt.gz 2019-02-10 03:41 2.4M
augustusGene.txt.gz 2015-07-26 13:13 1.7M
chromInfo.txt.gz 2012-06-28 23:09 1.7M
cytoBandIdeo.txt.gz 2013-04-28 14:30 1.6M
chromAlias.txt.gz 2018-08-05 06:25 1.4M
ensemblGeneScaffold.txt.gz 2019-02-10 03:41 863K
cpgIslandExt.txt.gz 2012-06-28 23:06 666K
cpgIslandExtUnmasked.txt.gz 2014-06-01 12:30 641K
microsat.txt.gz 2015-08-23 15:42 431K
ensGtp.txt.gz 2019-02-10 03:41 242K
ensemblToGeneName.txt.gz 2019-02-10 03:41 99K
ensemblSource.txt.gz 2019-02-10 03:41 74K
trackDb.txt.gz 2023-03-28 13:49 20K
gbLoaded.txt.gz 2020-08-21 15:32 14K
tableDescriptions.txt.gz 2024-11-16 02:03 5.4K
tableList.txt.gz 2024-11-17 03:31 2.3K
xenoRefSeqAli.sql 2020-08-21 15:32 2.1K
netHg19.sql 2012-07-29 11:23 2.1K
simpleRepeat.sql 2012-06-28 23:06 2.1K
trackDb.sql 2023-03-28 13:49 2.1K
netMm10.sql 2012-06-28 23:09 2.0K
xenoRefGene.sql 2020-08-21 15:32 2.0K
augustusGene.sql 2015-07-26 13:13 1.9K
ensGene.sql 2019-02-10 03:41 1.9K
nestedRepeats.sql 2012-06-28 23:07 1.9K
quality.sql 2012-06-28 23:07 1.9K
rmsk.sql 2012-06-28 23:08 1.8K
gold.sql 2012-06-28 23:09 1.8K
hgFindSpec.sql 2023-03-28 13:49 1.8K
xenoRefFlat.sql 2020-08-21 15:32 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 12:30 1.7K
chainHg19.sql 2012-07-29 11:18 1.7K
gap.sql 2012-06-28 23:19 1.7K
ensemblGeneScaffold.sql 2019-02-10 03:41 1.7K
history.txt.gz 2012-06-28 23:19 1.6K
chainMm10.sql 2012-06-28 23:14 1.6K
cpgIslandExt.sql 2012-06-28 23:06 1.6K
genscan.sql 2012-06-28 23:19 1.6K
gbLoaded.sql 2020-08-21 15:32 1.6K
tableList.sql 2024-11-17 03:31 1.6K
history.sql 2012-06-28 23:19 1.6K
chainHg19Link.sql 2012-07-29 11:19 1.5K
cytoBandIdeo.sql 2013-04-28 14:30 1.5K
genscanSubopt.sql 2012-06-28 23:06 1.5K
microsat.sql 2015-08-23 15:42 1.5K
chainMm10Link.sql 2012-06-28 23:10 1.5K
windowmaskerSdust.sql 2012-06-28 23:12 1.4K
tableDescriptions.sql 2024-11-16 02:03 1.4K
chromAlias.sql 2018-08-05 06:25 1.4K
ensGtp.sql 2019-02-10 03:41 1.4K
ensemblToGeneName.sql 2019-02-10 03:41 1.4K
bigFiles.sql 2024-11-17 03:31 1.4K
grp.sql 2014-03-02 03:40 1.4K
ensemblSource.sql 2019-02-10 03:41 1.4K
chromInfo.sql 2012-06-28 23:09 1.3K
ensPep.sql 2019-02-10 03:41 1.3K
gc5BaseBw.sql 2012-06-28 23:09 1.2K
hgFindSpec.txt.gz 2023-03-28 13:49 669
grp.txt.gz 2014-03-02 03:40 223
bigFiles.txt.gz 2024-11-17 03:31 68
gc5BaseBw.txt.gz 2012-06-28 23:09 63