quickload/C_sativa_DH55_Apr_2014/HEADER.md

<h1>Camelina sativa DH55 genome assembly</h1>
<body>
<p>
This directory contains annotation and sequence data files from the Camelina sativa DH55 genome assembly reported in Kogale et al 2014 - see http://www.nature.com/ncomms/2014/140423/ncomms4706/full/ncomms4706.html.
</p>
<p>Files are formatted for visualization in <a href="http://www.bioviz.org/igb">Integrated Genome Browser</a> (IGB). 
</p>
<p>
For details on data processing and analysis, see http://www.bitbucket.org/lorainelab/camelina.
</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>
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	22	<h1>Camelina sativa DH55 genome assembly</h1>
2			<body>
3			<p>
4			This directory contains annotation and sequence data files from the Camelina sativa DH55 genome assembly reported in Kogale et al 2014 - see http://www.nature.com/ncomms/2014/140423/ncomms4706/full/ncomms4706.html.
5			</p>
6			<p>Files are formatted for visualization in <a href="http://www.bioviz.org/igb">Integrated Genome Browser</a> (IGB).
7			</p>
8			<p>
9			For details on data processing and analysis, see http://www.bitbucket.org/lorainelab/camelina.
10			</p>
11			<p>
12			Files include:
13			</p>
14			<p>
15			<ul>
16			<li>
17			2bit file - sequence file in two-bit format, created using
18			faToTwoBit.
19			When users click <b>Load Sequence</b> buttons, IGB retrieves sequence data from this file. The 2bit file name must match the genome version.
20			To obtain a copy of faToTwoBit, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
21			</li>
22			<li>
23			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>.
24
25			<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>
26
27			<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>.)
28			</ul>
29			</p>
30			<p>
31			<b>Note:</b> Gene model annotation files have been re-formatted for fast transfer over the internet and for visualization in IGB.
32			</p>
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>