quickload/M_acuminata_DH_Pahang_Jan_2016/HEADER.md

<h1>Banana genome assembly</h1>
<body>

<p> This directory contains annotation and sequence data files from
the banana Musa acuminata DH Pahang version 2 genome assembly released January 2016. Files
are formatted for visualization in <a href="https://bioviz.org/">Integrated Genome Browser</a> (IGB).
</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="https://bioviz.org">Integrated Genome Browser</a>.

<li>genome.txt - meta-data file listing 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 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>Gene model annotation file(s) include:
<ul>
<li>M_acuminata_DH_Pahang_Jan_2016.bed.gz - gene models downloaded in GFF3 format from the <a href="http://banana-genome-hub.southgreen.fr/download">Banana Genome Hub download page</a> and converted to IGB-friendly format (BED-detail) using gff3ToBedDetail.py from this <a href="https://bitbucket.org/lorainelab/genomesource">git repository</a>. 
</li>
</ul>
<p>
For more information about quickload, visit <a href="https://bioviz.org">bioviz.org</a> and visit the on-line, searchable IGB User's Guide.
</p>
</body>
1	<h1>Banana genome assembly</h1>
2	<body>
3
4	<p> This directory contains annotation and sequence data files from
5	the banana Musa acuminata DH Pahang version 2 genome assembly released January 2016. Files
6	are formatted for visualization in <a href="https://bioviz.org/">Integrated Genome Browser</a> (IGB).
7	</p>
8
9	<p>
10	Files include:
11	</p>
12	<p>
13	<ul>
14	<li>
15	2bit file - sequence file in two-bit format, created using
16	faToTwoBit.
17	When users click <b>Load Sequence</b> buttons, IGB retrieves sequence data from this file. The 2bit file name must match the genome version.
18	To obtain a copy of faToTwoBit, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
19	</li>
20	<li>
21	annots.xml - meta-data file that lists available data sets and specifies how they will look once loaded into <a href="https://bioviz.org">Integrated Genome Browser</a>.
22
23	<li>genome.txt - meta-data file listing 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>
24
25	<li>reference gene model annotations 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>.)
26	</ul>
27	</p>
28	<p>
29	<b>Note:</b> Gene model annotation files have been re-formatted for fast transfer over the internet and for visualization in IGB.
30	</p>
31	<p>Gene model annotation file(s) include:
32	<ul>
33	<li>M_acuminata_DH_Pahang_Jan_2016.bed.gz - gene models downloaded in GFF3 format from the <a href="http://banana-genome-hub.southgreen.fr/download">Banana Genome Hub download page</a> and converted to IGB-friendly format (BED-detail) using gff3ToBedDetail.py from this <a href="https://bitbucket.org/lorainelab/genomesource">git repository</a>.
34	</li>
35	</ul>
36	<p>
37	For more information about quickload, visit <a href="https://bioviz.org">bioviz.org</a> and visit the on-line, searchable IGB User's Guide.
38	</p>
39	</body>