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	<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>