/[genomes]/quickload/A_lyrata_Apr_2011/HEADER.md
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Revision 5 - (show annotations)
Wed Sep 26 21:15:00 2018 UTC (2 years ago) by aloraine
File size: 1292 byte(s)
Add Arabidopsis lyrata genome assembly and annotations, from Phytozome
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>

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