/[genomes]/quickload/X_tropicalis_Jul_2016/HEADER.md
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Revision 115 - (hide annotations)
Sun Feb 16 03:49:40 2020 UTC (4 years, 9 months ago) by aloraine
File size: 1193 byte(s)
Add Xenopus tropicalis Jul 2016 assembly with RefSeq All (ncbiRefSeq) gene model annotations
1 aloraine 51 <html>
2     <body>
3 aloraine 115 <h1>JGI9.1/xenTro9 Xenopus tropicalis genome, Jul 2016 genome assembly</h1>
4 aloraine 51 <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 aloraine 79 Annotation (bed) and alignment (psl) files (if available) were downloaded from the UCSC Genome
10 aloraine 51 Bioinformatics Table Browser. Each file is named for its corresponding table in the
11     UCSC Genome database. See the <a href="annots.xml">annots.xml</a> meta-data file in
12     this directory for details.
13     </p>
14     <p>
15     Files with extension .gz were compressed and indexed using bgzip and
16 aloraine 79 tabix tools from <a href="https://www.htslib.org">htslib.org</a>.
17 aloraine 51 </p>
18     <p>
19 aloraine 115 The file named X_tropicalis_Jul_2016.2bit contains sequence data and is from the UCSC Genome
20 aloraine 80 Bioinformatics Web site. To convert a .2bit to fasta, use twoBitToFa. The file
21 aloraine 51 <a href="genome.txt">genome.txt</a> lists sequences and their sizes and was made from
22 aloraine 115 X_tropicalis_Jul_2016.2bit sequence file using twoBitInfo.
23 aloraine 51 </p>
24     <p>
25     Both twoBitInfo and twoBitToFa are
26     available from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
27     </p>
28     </body>
29     </html>

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