quickload/A_lyrata_Apr_2011/HEADER.md

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<h1>Arabidopsis lyrata (Apr 2011) version 1.0 (Aryl1) 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>
The gene model annotation file (A_lyrata_Apr_2011.bed.gz) was made from GFF and gene information files from Phytozome. 
</p>
<p>
The file named annotation.gtf.gz is from iPlant. It has been sorted, compressed with bgzip, and indexed using tabix for faster loading into IGB.
</p>
<p>
The file named A_lyrata_Apr_2011.2bit contains sequence data. It
was made from fasta file from iPlant/Ensembl. To convert it back
to fasta, use twoBitToFa. 
</p>
The file
<a href="genome.txt">genome.txt</a> lists sequences and their sizes and was made from the 2bit sequence file using twoBitInfo.
</p>
<p>
You can get twoBitInfo, twoBitToFa, faToTwoBit, and related programs from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
</p>
<p>
For more information about the sequence and annotation files, see the
repository
named <a href="https://bitbucket.org/aloraine/alyrata">Alyrata hosted
at BitBucket</a>. Also
see <a href="https://www.biostars.org/p/147826/">this Biostars
post</a>.
</p>
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1	aloraine	5	<html>
2			<body>
3			<h1>Arabidopsis lyrata (Apr 2011) version 1.0 (Aryl1) 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			The gene model annotation file (A_lyrata_Apr_2011.bed.gz) was made from GFF and gene information files from Phytozome.
10			</p>
11			<p>
12			The file named annotation.gtf.gz is from iPlant. It has been sorted, compressed with bgzip, and indexed using tabix for faster loading into IGB.
13			</p>
14			<p>
15			The file named A_lyrata_Apr_2011.2bit contains sequence data. It
16			was made from fasta file from iPlant/Ensembl. To convert it back
17			to fasta, use twoBitToFa.
18			</p>
19			The file
20			<a href="genome.txt">genome.txt</a> lists sequences and their sizes and was made from the 2bit sequence file using twoBitInfo.
21			</p>
22			<p>
23			You can get twoBitInfo, twoBitToFa, faToTwoBit, and related programs from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
24			</p>
25			<p>
26			For more information about the sequence and annotation files, see the
27			repository
28			named <a href="https://bitbucket.org/aloraine/alyrata">Alyrata hosted
29			at BitBucket</a>. Also
30			see <a href="https://www.biostars.org/p/147826/">this Biostars
31			post</a>.
32			</p>
33			</body>
34			</html>