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Revision 108 - (show annotations)
Tue Sep 10 20:35:41 2019 UTC (4 years, 10 months ago) by aloraine
File size: 1516 byte(s)
IGBF-1915 - Add water flea (Daphnia) genomes
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2 <body>
3 <h1>Daphnia magna (Apr 2010) water flea (Xinb3 v2.4) genome assembly</h1>
4 <p>
5 The files listed below are formatted for visualization in the Integrated Genome Browser, available from <a href="https://bioviz.org">BioViz.org</a>.
6 </p>
7 <p>
8 The file named D_magna_Apr_2010.2bit contains sequence data from <a href="ftp://ftp.ensemblgenomes.org/pub/metazoa/release-44/fasta/daphnia_magna/dna/Daphnia_magna.daphmag2.4.dna.toplevel.fa.gz">ftp://ftp.ensemblgenomes.org/pub/metazoa/release-44/fasta/daphnia_magna/dna/Daphnia_magna.daphmag2.4.dna.toplevel.fa.gz</a>. To convert a .2bit to fasta, use twoBitToFa. The file
9 <a href="genome.txt">genome.txt</a> lists sequences and their sizes and was made from
10 D_magna_Apr_2010.2bit sequence file using twoBitInfo. Both twoBitInfo and twoBitToFa are
11 available from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
12 </p>
13 <p>
14 The file named D_magna_Apr_2010.bed.gz contains gene models obtained from <a href="ftp://ftp.ensemblgenomes.org/pub/metazoa/release-44/gff3/daphnia_magna/Daphnia_magna.daphmag2.4.44.gff3.gz">ftp://ftp.ensemblgenomes.org/pub/metazoa/release-44/gff3/daphnia_magna/Daphnia_magna.daphmag2.4.44.gff3.gz</a>. Files with extension .gz were compressed and indexed using bgzip and
15 tabix tools from <a href="https://www.htslib.org">htslib.org</a>.
16 </p>
17 <p>
18 Data associated with paper: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15752432">wFleaBase: the Daphnia genome database</a>
19 </p>
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