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IGBF-1915 - Add water flea (Daphnia) genomes
| 1 | aloraine | 108 | <html> |
| 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> | ||
| 20 | </body> | ||
| 21 | </html> |
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