/[genomes]/quickload/P_trichocarpa_Aug_2012/HEADER.md
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Revision 46 - (hide annotations)
Thu Sep 27 15:23:52 2018 UTC (4 years ago) by aloraine
File size: 1078 byte(s)
Add Populus trichocarpa v2 and v3 genomes, collected from Phytozome
1 aloraine 46 <html>
2     <body>
3     <h1>Poplar genome version 3</h1>
4     <p>
5     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 file named P_trichocarpa_Aug_2012.bed.gz contains data reformatted from:
10     <ul>
11     <li>ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Ptrichocarpa/annotation/Ptrichocarpa_210_defline.txt
12     <li>ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Ptrichocarpa/annotation/Ptrichocarpa_210_gene_exons.gff3.gz
13     </ul>
14     <p>
15     See the <a href="annots.xml">annots.xml</a> meta-data file in this directory for
16     description and date of download.
17     </p>
18     <p>
19     Files with extension .gz were compressed and indexed using bgzip and
20     tabix tools from Heng Li.
21     </p>
22     <p>
23     The .2bit file contains sequence data reformatted from:
24     </p>
25     <p>
26     ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Ptrichocarpa/assembly/Ptrichocarpa_210.fa.gz
27     </p>
28     <p>
29     Re-formatting was done using twoBitToFa from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
30     </p>
31     </body>
32     </html>

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