/[genomes]/quickload/A_lyrata_Apr_2011/HEADER.md
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Revision 5 - (hide annotations)
Wed Sep 26 21:15:00 2018 UTC (5 years, 9 months ago) by aloraine
File size: 1292 byte(s)
Add Arabidopsis lyrata genome assembly and annotations, from Phytozome
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>

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