/[genomes]/quickload/T_rubripes_Oct_2011/HEADER.md
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Contents of /quickload/T_rubripes_Oct_2011/HEADER.md

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Revision 48 - (show annotations)
Thu Sep 27 15:29:58 2018 UTC (6 years ago) by aloraine
File size: 1247 byte(s)
Error occurred while calculating annotation data.
Add Takifugu rubripes (Oct 2011) Fugu (FUGU5/fr3) genome assembly and annotations from UCSC
1 <html>
2 <body>
3 <h1>Takifugu rubripes (Oct 2011) Fugu (FUGU5/fr3) 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 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 T_rubripes_Oct_2011.2bit contains sequence data and was downloaded from the UCSC Genome
20 Bioinformatics <a href="http://hgdownload-test.sdsc.edu/downloads.html">downloads
21 page</a>. To convert a .2bit to fasta, use twoBitToFa. The file
22 <a href="genome.txt">genome.txt</a> lists sequences and their sizes and was made from
23 T_rubripes_Oct_2011.2bit sequence file using twoBitInfo.
24 </p>
25 <p>
26 Both twoBitInfo and twoBitToFa are
27 available from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
28 </p>
29 </body>
30 </html>

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