/[genomes]/quickload/C_sativa_DH55_Apr_2014/HEADER.md
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Revision 22 - (show annotations)
Thu Sep 27 13:57:07 2018 UTC (2 years, 6 months ago) by aloraine
File size: 2028 byte(s)
Add Camelina sativa (false flax) April 2014 assembly
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>

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