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	<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>