/[genomes]/quickload/X_tropicalis_Jul_2016/HEADER.md
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quickload/X_tropicalis_Nov_2009/HEADER.md revision 51 by aloraine, Thu Sep 27 15:37:21 2018 UTC quickload/X_tropicalis_Jul_2016/HEADER.md revision 115 by aloraine, Sun Feb 16 03:49:40 2020 UTC
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1  <html>  <html>
2  <body>  <body>
3  <h1>JGI4.2/xenTro3 Xenopus tropicalis genome, Nov 2009 genome assembly</h1>  <h1>JGI9.1/xenTro9 Xenopus tropicalis genome, Jul 2016 genome assembly</h1>
4  <p>  <p>
5  The files listed below are formatted for visualization in the Integrated Genome  The files listed below are formatted for visualization in the Integrated Genome
6  Browser, available from <a href="https://bioviz.org">BioViz.org</a>.  Browser, available from <a href="https://bioviz.org">BioViz.org</a>.
7  </p>  </p>
8  <p>  <p>
9  Annotation (bed) and alignment (psl) files were downloaded from the UCSC Genome  Annotation (bed) and alignment (psl) files (if available) were downloaded from the UCSC Genome
10  Bioinformatics Table Browser. Each file is named for its corresponding table in the  Bioinformatics Table Browser. Each file is named for its corresponding table in the
11  UCSC Genome database. See the <a href="annots.xml">annots.xml</a> meta-data file in  UCSC Genome database. See the <a href="annots.xml">annots.xml</a> meta-data file in
12  this directory for details.  this directory for details.
13  </p>  </p>
14  <p>  <p>
15  Files with extension .gz were compressed and indexed using bgzip and  Files with extension .gz were compressed and indexed using bgzip and
16  tabix tools from <a href="https://www.htslib.org>htslib.org</a>.  tabix tools from <a href="https://www.htslib.org">htslib.org</a>.
17  </p>  </p>
18  <p>  <p>
19  The file named X_tropicalis_Nov_2009.2bit contains sequence data and was downloaded from the UCSC Genome  The file named X_tropicalis_Jul_2016.2bit contains sequence data and is from the UCSC Genome
20  Bioinformatics <a href="http://hgdownload-test.sdsc.edu/downloads.html">downloads  Bioinformatics Web site. To convert a .2bit to fasta, use twoBitToFa. The file
 page</a>. To convert a .2bit to fasta, use twoBitToFa. The file  
21  <a href="genome.txt">genome.txt</a> lists sequences and their sizes and was made from  <a href="genome.txt">genome.txt</a> lists sequences and their sizes and was made from
22  X_tropicalis_Nov_2009.2bit sequence file using twoBitInfo.  X_tropicalis_Jul_2016.2bit sequence file using twoBitInfo.
23  </p>  </p>
24  <p>  <p>
25  Both twoBitInfo and twoBitToFa are  Both twoBitInfo and twoBitToFa are
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