quickload/P_patens_Jan_2018/HEADER.md

<h1>Physcomitrella patens (moss) January 2018 genome assembly</h1>
<body>
<p>
This directory contains annotation and sequence data files from the Physcomitrella patens genome version 3.3 genome released in January 2018. 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. 
</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>
<li>genome.txt - meta-data file that lists genomic sequences and their sizes, created using twoBitInfo using the 2bit file.
</li>
<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>.)
</li>
</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. Gene model annotation files use BED-detail format, which is the same as BED12 but contains two additional fields: field 13 contains the locus identifier and field 14 contains descriptive text.
</p>
<p>
To get faToTwoBit and twoBitInfo, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
</body>
1	<h1>Physcomitrella patens (moss) January 2018 genome assembly</h1>
2	<body>
3	<p>
4	This directory contains annotation and sequence data files from the Physcomitrella patens genome version 3.3 genome released in January 2018. Files are formatted for visualization in <a href="https://bioviz.org">Integrated Genome Browser</a> (IGB).
5	</p>
6	<p>
7	Files include:
8	</p>
9	<p>
10	<ul>
11	<li>
12	2bit file - sequence file in two-bit format, created using
13	faToTwoBit.
14	When users click <b>Load Sequence</b> buttons, IGB retrieves sequence data from this file.
15	</li>
16	<li>
17	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>.
18	</li>
19	<li>genome.txt - meta-data file that lists genomic sequences and their sizes, created using twoBitInfo using the 2bit file.
20	</li>
21	<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>.)
22	</li>
23	</ul>
24	</p>
25	<p>
26	<b>Note:</b> Gene model annotation files have been re-formatted for fast transfer over the internet and for visualization in IGB. Gene model annotation files use BED-detail format, which is the same as BED12 but contains two additional fields: field 13 contains the locus identifier and field 14 contains descriptive text.
27	</p>
28	<p>
29	To get faToTwoBit and twoBitInfo, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
30	</body>