This directory contains the Jul. 2010 (Broad Institute Myoluc2.0/myoLuc2) assembly of the microbat genome (myoLuc2, Broad Institute (NCBI Project ID: 16951, Accession: GCA_000147115.1)), as well as repeat annotations and GenBank sequences. This assembly was produced by Broad Institute of MIT and Harvard. For more information on the microbat genome, see the project website: http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=16951 Files included in this directory: myoLuc2.2bit - contains the complete microbat/myoLuc2 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 myoLuc2.agp.gz - Description of how the assembly was generated from fragments. myoLuc2.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. myoLuc2.fa.masked.gz - "Hard-masked" assembly sequence in one file. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. myoLuc2.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) myoLuc2.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. md5sum.txt - checksums of files in this directory mrna.fa.gz - Microbat 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. myoLuc2.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. myoLuc2.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used - to construct the GC Percent track myoLuc2.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 myoLuc2.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 myoLuc2.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/myoLuc2/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/myoLuc2/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/myoLuc2/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/myoLuc2/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/myoLuc2/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 All the tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory - genes/ 2020-10-02 13:38 - md5sum.txt 2019-01-17 15:56 479 mrna.fa.gz 2019-10-16 11:45 13K mrna.fa.gz.md5 2019-10-16 11:45 45 myoLuc2.2bit 2010-11-03 15:44 507M myoLuc2.agp.gz 2011-06-30 14:28 1.7M myoLuc2.chrom.sizes 2010-11-02 15:07 198K myoLuc2.chromAlias.txt 2020-09-29 10:49 597K myoLuc2.fa.gz 2011-06-30 14:39 621M myoLuc2.fa.masked.gz 2011-06-30 14:48 419M myoLuc2.fa.out.gz 2011-06-30 14:29 99M myoLuc2.gc5Base.wib 2019-01-17 14:50 380M myoLuc2.gc5Base.wig.gz 2019-01-17 14:50 7.8M myoLuc2.gc5Base.wigVarStep.gz 2010-11-02 15:13 1.0G myoLuc2.trf.bed.gz 2011-06-30 14:29 4.8M upstream1000.fa.gz 2019-10-16 11:56 332K upstream1000.fa.gz.md5 2019-10-16 11:56 53 upstream2000.fa.gz 2019-10-16 11:56 632K upstream2000.fa.gz.md5 2019-10-16 11:56 53 upstream5000.fa.gz 2019-10-16 11:56 1.5M upstream5000.fa.gz.md5 2019-10-16 11:56 53 xenoMrna.fa.gz 2019-10-16 11:55 6.8G xenoMrna.fa.gz.md5 2019-10-16 11:55 49 xenoRefMrna.fa.gz 2019-10-16 11:56 331M xenoRefMrna.fa.gz.md5 2019-10-16 11:56 52