/[genomes]/quickload/X_tropicalis_Nov_2009/HEADER.md
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Revision 51 - (show annotations)
Thu Sep 27 15:37:21 2018 UTC (2 years, 6 months ago) by aloraine
File size: 1256 byte(s)
Add JGI4.2/xenTro3 Xenopus tropicalis genome, Nov 2009 genome assembly and annotations, collected from UCSC
1 <html>
2 <body>
3 <h1>JGI4.2/xenTro3 Xenopus tropicalis genome, Nov 2009 genome assembly</h1>
4 <p>
5 The files listed below are formatted for visualization in the Integrated Genome
6 Browser, available from <a href="https://bioviz.org">BioViz.org</a>.
7 </p>
8 <p>
9 Annotation (bed) and alignment (psl) files were downloaded from the UCSC Genome
10 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
12 this directory for details.
13 </p>
14 <p>
15 Files with extension .gz were compressed and indexed using bgzip and
16 tabix tools from <a href="https://www.htslib.org>htslib.org</a>.
17 </p>
18 <p>
19 The file named X_tropicalis_Nov_2009.2bit contains sequence data and was downloaded from the UCSC Genome
20 Bioinformatics <a href="http://hgdownload-test.sdsc.edu/downloads.html">downloads
21 page</a>. To convert a .2bit to fasta, use twoBitToFa. The file
22 <a href="genome.txt">genome.txt</a> lists sequences and their sizes and was made from
23 X_tropicalis_Nov_2009.2bit sequence file using twoBitInfo.
24 </p>
25 <p>
26 Both twoBitInfo and twoBitToFa are
27 available from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
28 </p>
29 </body>
30 </html>

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