/[genomes]/quickload/P_trichocarpa_Aug_2012/HEADER.md
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Contents of /quickload/P_trichocarpa_Aug_2012/HEADER.md

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Revision 46 - (show annotations)
Thu Sep 27 15:23:52 2018 UTC (3 years, 2 months ago) by aloraine
File size: 1078 byte(s)
Add Populus trichocarpa v2 and v3 genomes, collected from Phytozome
1 <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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