quickload/X_tropicalis_Nov_2009/HEADER.md

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<h1>JGI4.2/xenTro3 Xenopus tropicalis genome, Nov 2009 genome assembly</h1>
<p>
The files listed below are formatted for visualization in the Integrated Genome
Browser, available from <a href="https://bioviz.org">BioViz.org</a>.
</p>
<p>
Annotation (bed) and alignment (psl) files (if available) were downloaded from the UCSC Genome
Bioinformatics Table Browser. Each file is named for its corresponding table in the
UCSC Genome database. See the <a href="annots.xml">annots.xml</a> meta-data file in
this directory for details.
</p>
<p>
Files with extension .gz were compressed and indexed using bgzip and
tabix tools from <a href="https://www.htslib.org">htslib.org</a>.
</p>
<p>
The file named X_tropicalis_Nov_2009.2bit contains sequence data and was downloaded from the UCSC Genome
Bioinformatics <a href="http://hgdownload-test.sdsc.edu/downloads.html">downloads
page</a>. To convert a .2bit to fasta, use twoBitToFa. The file
<a href="genome.txt">genome.txt</a> lists sequences and their sizes and was made from 
X_tropicalis_Nov_2009.2bit sequence file using twoBitInfo.
</p>
<p>
Both twoBitInfo and twoBitToFa are
available from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
</p>
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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			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>