quickload/R_norvegicus_Mar_2012/HEADER.md

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<h1>Rattus norvegicus (Mar 2012) rat (RGSC 5.0/rn5) genome assembly</h1>
<p>
The files listed below are formatted for visualization in the Integrated Genome
Browser, available from <a href="https://bioviz.org">BioViz.org</a>.
</p>
<p>
Annotation (bed) and alignment (psl) files (if available) were downloaded from the UCSC Genome
Bioinformatics Table Browser. Each file is named for its corresponding table in the
UCSC Genome database. See the <a href="annots.xml">annots.xml</a> meta-data file in
this directory for details.
</p>
<p>
Files with extension .gz were compressed and indexed using bgzip and
tabix tools from <a href="https://www.htslib.org">htslib.org</a>.
</p>
<p>
The file named R_norvegicus_Mar_2012.2bit contains sequence data and is from the UCSC Genome
Bioinformatics Web site. To convert a .2bit to fasta, use twoBitToFa. The file
<a href="genome.txt">genome.txt</a> lists sequences and their sizes and was made from 
R_norvegicus_Mar_2012.2bit sequence file using twoBitInfo.
</p>
<p>
Both twoBitInfo and twoBitToFa are
available from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
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1	aloraine	50	<html>
2			<body>
3	aloraine	86	<h1>Rattus norvegicus (Mar 2012) rat (RGSC 5.0/rn5) genome assembly</h1>
4	aloraine	50	<p>
5			The files listed below are formatted for visualization in the Integrated Genome
6			Browser, available from <a href="https://bioviz.org">BioViz.org</a>.
7			</p>
8			<p>
9	aloraine	79	Annotation (bed) and alignment (psl) files (if available) were downloaded from the UCSC Genome
10	aloraine	50	Bioinformatics Table Browser. Each file is named for its corresponding table in the
11			UCSC Genome database. See the <a href="annots.xml">annots.xml</a> meta-data file in
12			this directory for details.
13			</p>
14			<p>
15			Files with extension .gz were compressed and indexed using bgzip and
16	aloraine	79	tabix tools from <a href="https://www.htslib.org">htslib.org</a>.
17	aloraine	50	</p>
18			<p>
19	aloraine	80	The file named R_norvegicus_Mar_2012.2bit contains sequence data and is from the UCSC Genome
20			Bioinformatics Web site. To convert a .2bit to fasta, use twoBitToFa. The file
21	aloraine	50	<a href="genome.txt">genome.txt</a> lists sequences and their sizes and was made from
22			R_norvegicus_Mar_2012.2bit sequence file using twoBitInfo.
23			</p>
24			<p>
25			Both twoBitInfo and twoBitToFa are
26			available from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
27			</p>
28			</body>
29			</html>