This directory contains the March 2009 (WUGSC 3.2/calJac3) assembly of
the marmoset genome (calJac3, WUSTL 3.2 (GCA_000004665.1)),
as well as repeat annotations and GenBank sequences.
This assembly was produced by the Washington University St. Louis (WUSTL)
School of Medicine Genome Sequencing Center in St. Louis.
For more information on the marmoset genome, see the project website:
http://genome.wustl.edu/genomes/view/callithrix_jacchus/
Files included in this directory:
calJac3.2bit - contains the complete marmoset/calJac3 genome sequence
in the 2bit file format. The utility program, twoBitToFa (available
from the kent src tree), can be used to extract .fa file(s) from
this file. A pre-compiled version of the command line tool can be
found at:
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
See also:
http://genome.ucsc.edu/admin/cvs.html
http://genome.ucsc.edu/admin/jk-install.html
calJac3.agp.gz - Description of how the assembly was generated from
fragments.
calJac3.fa.gz - "Soft-masked" assembly sequence in one file.
Repeats from RepeatMasker and Tandem Repeats Finder (with period
of 12 or less) are shown in lower case; non-repeating sequence is
shown in upper case.
calJac3.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
calJac3.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. *** PLEASE ADD REPEATMASKER VERSION AND LIB VERSION FROM THE DATE THAT REPEATMASKER WAS RUN (MAY BE IN MAKE.DOC)
calJac3.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
format.
est.fa.gz - Marmoset ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Marmoset mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
xenoMrna.fa.gz - GenBank mRNAs from species other than that of
the genome. This sequence data is updated once a week via automatic
GenBank updates.
calJac3.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
calJac3.chromAlias.txt - sequence name alias file, one line
for each sequence name. First column is sequence name followed by
tab separated alias names.
------------------------------------------------------------------
If you plan to download a large file or multiple files from this
directory, we recommend that you use ftp rather than downloading the
files via our website. To do so, ftp to hgdownload.cse.ucsc.edu
[username: anonymous, password: your email address], then cd to the
directory goldenPath/calJac3/bigZips. 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/calJac3/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/calJac3/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/calJac3/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/calJac3/bigZips/chromFa.tar.gz'
-O chromFa.tar.gz
To unpack the *.tar.gz files:
tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
gunzip <file>.fa.gz
The Marmoset sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, 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 these data
if the providers of these data are properly acknowledged. See
http://genome.ucsc.edu/goldenPath/credits.html for credit information.
3. The centers producing the data reserve 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.
Name Last modified Size Description
Parent Directory -
calJac3.2bit 2010-02-09 14:51 727M
calJac3.agp.gz 2010-03-31 14:29 5.1M
calJac3.chrom.sizes 2010-02-04 16:24 328K
calJac3.chromAlias.bb 2022-09-08 14:10 4.3M
calJac3.chromAlias.txt 2022-09-08 14:10 830K
calJac3.fa.gz 2010-03-31 14:43 865M
calJac3.fa.masked.gz 2010-03-31 14:51 478M
calJac3.fa.out.gz 2010-03-31 14:30 154M
calJac3.trf.bed.gz 2010-03-31 14:30 5.2M
est.fa.gz 2019-10-14 22:38 63M
est.fa.gz.md5 2019-10-14 22:38 44
genes/ 2020-02-05 13:46 -
md5sum.txt 2010-05-17 12:42 304
mrna.fa.gz 2019-10-14 22:25 347K
mrna.fa.gz.md5 2019-10-14 22:25 45
refMrna.fa.gz 2019-10-14 22:39 165K
refMrna.fa.gz.md5 2019-10-14 22:39 48
upstream1000.fa.gz 2019-10-14 22:40 6.4M
upstream1000.fa.gz.md5 2019-10-14 22:40 53
upstream2000.fa.gz 2019-10-14 22:40 12M
upstream2000.fa.gz.md5 2019-10-14 22:40 53
upstream5000.fa.gz 2019-10-14 22:41 28M
upstream5000.fa.gz.md5 2019-10-14 22:41 53
xenoMrna.fa.gz 2019-10-14 22:34 6.8G
xenoMrna.fa.gz.md5 2019-10-14 22:34 49
xenoRefMrna.fa.gz 2019-10-14 22:39 331M
xenoRefMrna.fa.gz.md5 2019-10-14 22:39 52