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	<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>