quickload/O_sativa_japonica_Oct_2011/HEADER.md

<h1>Oryza sativa japonica genome assembly</h1>
<body>
<p>
This directory contains annotation and sequence data files from rice genome assembly Os-Nipponbare-Reference-IRGSP-1.0 released October 2011. Files are formatted for visualization in <a href="https://bioviz.org">Integrated Genome Browser</a> (IGB). 
</p>
<p>
Files include:
</p>
<p>
<ul>
<li>
2bit file - sequence file in two-bit format, created using
faToTwoBit. 
When users click <b>Load Sequence</b> buttons, IGB retrieves sequence data from this file. The 2bit file name must match the genome version.
To obtain a copy of faToTwoBit, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>. 
</li>
<li>
annots.xml - meta-data file that lists available data sets and specifies how they will look once loaded into <a href="http://bioviz.org/igb">Integrated Genome Browser</a>.

<li>genome.txt - meta-data file that lists genomic sequences and their sizes, created using twoBitInfo using the 2bit file. To obtain a copy of twoBitInfo, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>

<li>reference gene model annotations in bed or bed detail format, compressed using bgzip and indexed using tabix (See: <a href="http://bioinformatics.oxfordjournals.org/content/27/5/718">Tabix: fast retrieval of sequence features from generic TAB-delimited files</a> and <a href="http://genome.ucsc.edu/FAQ/FAQformat.html">http://genome.ucsc.edu/FAQ/FAQformat.html</a>.)
</ul>
</p>
<p>
<b>Note:</b> Gene model annotation files have been re-formatted for fast transfer over the internet and for visualization in IGB. 
</p>
<p>Gene model annotation files include:
<ul>
<li>O_sativa_japonica_Oct_2011.bed.gz - RGAP/MSU7 gene models, from the <a href="http://rice.plantbiology.msu.edu">Rice Genome Annotation Project</a> at MSU.
<li>IRGSP-1.0_representative_2013-04-24.bed.gz - From the Rice Annotation Project Database <a href="http://rapdb.dna.affrc.go.jp/">RAP-Db</a>.
</ul>
<p>
For more information about quickload, visit <a href="http://www.bioviz.org/igb">bioviz.org/igb</a> and visit the on-line, searchable IGB User's Guide.
</p>
</body>
1	aloraine	43	<h1>Oryza sativa japonica genome assembly</h1>
2			<body>
3			<p>
4			This directory contains annotation and sequence data files from rice genome assembly Os-Nipponbare-Reference-IRGSP-1.0 released October 2011. Files are formatted for visualization in <a href="https://bioviz.org">Integrated Genome Browser</a> (IGB).
5			</p>
6			<p>
7			Files include:
8			</p>
9			<p>
10			<ul>
11			<li>
12			2bit file - sequence file in two-bit format, created using
13			faToTwoBit.
14			When users click <b>Load Sequence</b> buttons, IGB retrieves sequence data from this file. The 2bit file name must match the genome version.
15			To obtain a copy of faToTwoBit, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
16			</li>
17			<li>
18			annots.xml - meta-data file that lists available data sets and specifies how they will look once loaded into <a href="http://bioviz.org/igb">Integrated Genome Browser</a>.
19
20			<li>genome.txt - meta-data file that lists genomic sequences and their sizes, created using twoBitInfo using the 2bit file. To obtain a copy of twoBitInfo, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>
21
22			<li>reference gene model annotations in bed or bed detail format, compressed using bgzip and indexed using tabix (See: <a href="http://bioinformatics.oxfordjournals.org/content/27/5/718">Tabix: fast retrieval of sequence features from generic TAB-delimited files</a> and <a href="http://genome.ucsc.edu/FAQ/FAQformat.html">http://genome.ucsc.edu/FAQ/FAQformat.html</a>.)
23			</ul>
24			</p>
25			<p>
26			<b>Note:</b> Gene model annotation files have been re-formatted for fast transfer over the internet and for visualization in IGB.
27			</p>
28			<p>Gene model annotation files include:
29			<ul>
30			<li>O_sativa_japonica_Oct_2011.bed.gz - RGAP/MSU7 gene models, from the <a href="http://rice.plantbiology.msu.edu">Rice Genome Annotation Project</a> at MSU.
31			<li>IRGSP-1.0_representative_2013-04-24.bed.gz - From the Rice Annotation Project Database <a href="http://rapdb.dna.affrc.go.jp/">RAP-Db</a>.
32			</ul>
33			<p>
34			For more information about quickload, visit <a href="http://www.bioviz.org/igb">bioviz.org/igb</a> and visit the on-line, searchable IGB User's Guide.
35			</p>
36			</body>