quickload/G_gallus_Nov_2011/HEADER.md

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<h1>Gallus gallus (Nov 2011) chicken (galGal4/ICGC Gallus-gallus-4.0) 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 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 G_gallus_Nov_2011.2bit contains sequence data and was downloaded from the UCSC Genome
Bioinformatics <a href="http://hgdownload-test.sdsc.edu/downloads.html">downloads
page</a>. 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 
G_gallus_Nov_2011.2bit 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>.
</p>
</body>
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1	<html>
2	<body>
3	<h1>Gallus gallus (Nov 2011) chicken (galGal4/ICGC Gallus-gallus-4.0) genome assembly</h1>
4	<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	Annotation (bed) and alignment (psl) files were downloaded from the UCSC Genome
10	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	tabix tools from <a href="https://www.htslib.org>htslib.org</a>.
17	</p>
18	<p>
19	The file named G_gallus_Nov_2011.2bit contains sequence data and was downloaded from the UCSC Genome
20	Bioinformatics <a href="http://hgdownload-test.sdsc.edu/downloads.html">downloads
21	page</a>. To convert a .2bit to fasta, use twoBitToFa. The file
22	<a href="genome.txt">genome.txt</a> lists sequences and their sizes and was made from
23	G_gallus_Nov_2011.2bit sequence file using twoBitInfo.
24	</p>
25	<p>
26	Both twoBitInfo and twoBitToFa are
27	available from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
28	</p>
29	</body>
30	</html>