/[genomes]/quickload/O_sativa_japonica_Oct_2011/HEADER.md
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Revision 43 - (show annotations)
Thu Sep 27 15:15:02 2018 UTC (13 months, 2 weeks ago) by aloraine
File size: 2189 byte(s)
Add Oryza sativa japonica June 2009 and Oryza sativa japonica variety Os-Nipponbare-Reference-IRGSP-1.0 genome assemblies and annotations
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>

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