/[genomes]/quickload/X_tropicalis_Jul_2016/HEADER.md
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Contents of /quickload/X_tropicalis_Jul_2016/HEADER.md

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Revision 115 - (show annotations)
Sun Feb 16 03:49:40 2020 UTC (2 years, 5 months ago) by aloraine
File size: 1193 byte(s)
Add Xenopus tropicalis Jul 2016 assembly with RefSeq All (ncbiRefSeq) gene model annotations
1 <html>
2 <body>
3 <h1>JGI9.1/xenTro9 Xenopus tropicalis genome, Jul 2016 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 Annotation (bed) and alignment (psl) files (if available) were downloaded from the UCSC Genome
10 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 tabix tools from <a href="https://www.htslib.org">htslib.org</a>.
17 </p>
18 <p>
19 The file named X_tropicalis_Jul_2016.2bit contains sequence data and is from the UCSC Genome
20 Bioinformatics Web site. To convert a .2bit to fasta, use twoBitToFa. The file
21 <a href="genome.txt">genome.txt</a> lists sequences and their sizes and was made from
22 X_tropicalis_Jul_2016.2bit sequence file using twoBitInfo.
23 </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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