This directory contains the June 2007 assembly of the marmoset genome (calJac1, WUSTL Callithrix_jacchus-2.0.2), as well as repeat annotations and GenBank sequences. This assembly was produced by the Genome Sequencing Center at the Washington University School of Medicine in St. Louis. For more information on the marmoset genome, see the project website: http://genome.wustl.edu/genome.cgi?GENOME=Callithrix%20jacchus Files included in this directory: calJac1.2bit - contains the complete marmoset/calJac1 genome sequence in the 2bit file format. 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. 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/git.html http://genome.ucsc.edu/admin/jk-install.html calJac1.agp.gz - Description of how the assembly was generated from fragments. calJac1.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. calJac1.fa.masked.gz - "Hard-masked" assembly sequence in one file. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. calJac1.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the -s (sensitive) setting. Repeat Masker version: # May 17 2007 (open-3-1-8) version of RepeatMasker Repeat Masker library version: RELEASE 20061006; calJac1.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. calJac1.quals.fa.gz - quality scores in fasta file format 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. upstream1000.fa.gz - Sequences 1000 bases upstream of annotated transcription starts for Xeno RefSeq genes with annotated 5' UTRs. This file is updated weekly so it could be slightly out of sync with the Xeno RefSeq data which is updated daily for most assemblies. upstream2000.fa.gz - Same as upstream1000, but 2000 bases. upstream5000.fa.gz - Same as upstream1000, but 5000 bases. 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. calJac1.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. ------------------------------------------------------------------ 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, then go to the directory goldenPath/calJac1/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/calJac1/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/calJac1/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/calJac1/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/calJac1/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. It is requested that users of this marmoset sequence assembly acknowledge the Washington University School of Medicine, Genome Sequencing Center in any publications that result from use of this sequence assembly. 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 - calJac1.2bit 2007-09-05 14:44 757M calJac1.agp.gz 2008-01-11 09:59 6.1M calJac1.chrom.sizes 2007-08-21 14:54 845K calJac1.fa.gz 2008-01-11 10:14 912M calJac1.fa.masked.gz 2008-01-11 10:23 505M calJac1.fa.out.gz 2008-01-11 10:00 158M calJac1.quals.fa.gz 2009-06-08 14:07 535M calJac1.trf.bed.gz 2008-01-11 10:00 5.6M est.fa.gz 2019-10-16 19:58 63M est.fa.gz.md5 2019-10-16 19:58 44 genes/ 2020-02-05 13:46 - md5sum.txt 2014-01-03 15:02 358 mrna.fa.gz 2019-10-16 19:54 347K mrna.fa.gz.md5 2019-10-16 19:54 45 refMrna.fa.gz 2019-10-16 19:59 165K refMrna.fa.gz.md5 2019-10-16 19:59 48 upstream1000.fa.gz 2019-10-16 20:00 16M upstream1000.fa.gz.md5 2019-10-16 20:00 53 upstream2000.fa.gz 2019-10-16 20:01 31M upstream2000.fa.gz.md5 2019-10-16 20:01 53 upstream5000.fa.gz 2019-10-16 20:02 86M upstream5000.fa.gz.md5 2019-10-16 20:02 53 xenoMrna.fa.gz 2016-03-22 20:45 5.0G xenoMrna.fa.gz.md5 2016-03-22 20:46 49 xenoRefMrna.fa.gz 2019-10-16 19:59 331M xenoRefMrna.fa.gz.md5 2019-10-16 19:59 52