/[genomes]/quickload/C_sativa_DH55_Apr_2014/HEADER.md
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Revision 22 - (hide annotations)
Thu Sep 27 13:57:07 2018 UTC (5 years, 6 months ago) by aloraine
File size: 2028 byte(s)
Add Camelina sativa (false flax) April 2014 assembly
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>

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