This directory contains the Oct. 2010 (WS220/ce10) assembly of the C. elegans genome (ce10, Washington University School of Medicine GSC and Sanger Institute WS220), as well as repeat annotations and GenBank sequences. This assembly was produced by the Genome Sequencing Center at the Washington University in St. Louis (WUSTL) School of Medicine and the Sanger Institute. For more information on the C. elegans genome, see the WUSTL project website at http://genome.wustl.edu/genome.cgi?GENOME=Caenorhabditis+elegans. and WormBase information: http://wiki.wormbase.org/index.php/Caenorhabditis_elegans This UCSC sequence data was downloaded from: ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_elegans/ Files included in this directory: ce10.2bit - contains the complete C. elegans/ce10 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 chromAgp.tar.gz - Description of how the assembly was generated from fragments, unpacking to one file per chromosome. chromFa.tar.gz - The assembly sequence in one file per chromosome. 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. chromFaMasked.tar.gz - The assembly sequence in one file per chromosome. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. chromOut.tar.gz - RepeatMasker .out files (one file per chromosome). RepeatMasker was run with the -s (sensitive) setting. RepeatMasker version: June 30 2010 (open-3-2-9) version of RepeatMasker CC RELEASE 20090604 chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into UCSC's BED 5+ format (one file per chromosome). est.fa.gz - C. elegans 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 - C. elegans mRNA from GenBank. This sequence data is updated once a week via automatic GenBank updates. refMrna.fa.gz - RefSeq mRNA from the same species as the genome. This sequence data is updated once a week via automatic GenBank updates. upstream1000.fa.gz - Sequences 1000 bases upstream of annotated transcription starts of RefSeq genes with annotated 5' UTRs. This file is updated weekly so it might be slightly out of sync with the 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. ce10.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. ce10.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used - to construct the GC Percent track ce10.gc5Base.wig.gz - wiggle database table for the GC Percent track - this is an older standard alternative to the current - bigWig format of the track, sometimes usefull for analysis ce10.gc5Base.wib - binary data to correspond with the gc5Base.wig file see also: http://genome.ucsc.edu/goldenPath/help/wiggle.html and http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database for a discussion of how to use the wig.gz and .wib files for interaction with the GC percent data values ------------------------------------------------------------------ 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/ce10/bigZips. To download multiple files, use the "mget" command: mget ... - 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/ce10/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/ce10/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/ce10/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/ce10/bigZips/chromFa.tar.gz' -O chromFa.tar.gz To unpack the *.tar.gz files: tar xvzf .tar.gz To uncompress the fa.gz files: gunzip .fa.gz ------------------------------------------------------------------------ The C. elegans sequence is made freely available to the community by the Genome Sequencing Center at the WUSTL School of Medicine. Please see the WUSTL data use policy at http://genome.wustl.edu/data.cgi for data use restrictions and citation information. ------------------------------------------------------------------------