/[genomes]/quickload/X_tropicalis_Nov_2009/HEADER.md
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Revision 80 - (hide annotations)
Sat Oct 27 01:44:05 2018 UTC (2 years, 3 months ago) by aloraine
File size: 1193 byte(s)
Remove broken link to UCSC downloads page (it moved)
1 aloraine 51 <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 aloraine 79 Annotation (bed) and alignment (psl) files (if available) were downloaded from the UCSC Genome
10 aloraine 51 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 aloraine 79 tabix tools from <a href="https://www.htslib.org">htslib.org</a>.
17 aloraine 51 </p>
18     <p>
19 aloraine 80 The file named X_tropicalis_Nov_2009.2bit contains sequence data and is from the UCSC Genome
20     Bioinformatics Web site. To convert a .2bit to fasta, use twoBitToFa. The file
21 aloraine 51 <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.
23     </p>
24     <p>
25     Both twoBitInfo and twoBitToFa are
26     available from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
27     </p>
28     </body>
29     </html>

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