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 22:08 4.3M calJac3.chromAlias.txt 2022-09-08 22:08 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 2020-02-27 00:47 63M est.fa.gz.md5 2020-02-27 00:47 44 genes/ 2020-02-05 13:46 - md5sum.txt 2022-09-08 22:01 417 mrna.fa.gz 2020-02-27 00:33 349K mrna.fa.gz.md5 2020-02-27 00:33 45 refMrna.fa.gz 2020-02-27 00:48 165K refMrna.fa.gz.md5 2020-02-27 00:48 48 upstream1000.fa.gz 2020-02-27 00:49 6.4M upstream1000.fa.gz.md5 2020-02-27 00:49 53 upstream2000.fa.gz 2020-02-27 00:49 12M upstream2000.fa.gz.md5 2020-02-27 00:49 53 upstream5000.fa.gz 2020-02-27 00:49 28M upstream5000.fa.gz.md5 2020-02-27 00:49 53 xenoMrna.fa.gz 2020-02-27 00:43 6.8G xenoMrna.fa.gz.md5 2020-02-27 00:43 49 xenoRefMrna.fa.gz 2020-02-27 00:48 336M xenoRefMrna.fa.gz.md5 2020-02-27 00:48 52