/[genomes]/quickload/D_melanogaster_Jul_2014/HEADER.md
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Revision 25 - (hide annotations)
Thu Sep 27 14:02:56 2018 UTC (4 years, 2 months ago) by aloraine
File size: 1468 byte(s)
Add Drosophila melanogaster (Jul 2014) fruit fly (dmel_r6.03_FB2014_06) assembly, collected from FlyBase
1 aloraine 25 <html>
2     <body>
3     <h1>Drosophila melanogaster (Jul 2014) fruit fly (dmel_r6.03_FB2014_06/BDGP6) 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     The gene model annotation file (D_melanogaster_Jul_2014.bed.gz) was made from a GTF file
10     downloaded Nov. 22, 2014 from <a
11     href="ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.03_FB2014_06/gtf">ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.03_FB2014_06
12     /gtf</a>.
13     </p>
14     <p>
15     The file named D_melanogaster_Jul_2014.2bit contains sequence data. It
16     was made from fasta file named dmel-all-chromosome-r6.03.fasta.gz
17     downloaded
18     from <a href="ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.03_FB2014_06/fasta/">ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.03_FB2014_06/fasta</a>. To convert it back
19     to fasta, use twoBitToFa.
20     </p>
21     The file
22     <a href="genome.txt">genome.txt</a> lists sequences and their sizes and was made from
23     D_melanogaster_Jul_2014.2bit sequence file using twoBitInfo.
24     </p>
25     <p>
26     For more information,
27     see <a href="http://lorainelab.org/?p=457">this post</a>
28     at <a href="http://www.lorainelab.org">LoraineLab.org</a>.
29     </p>
30     <p>
31     You can get twoBitInfo, twoBitToFa, faToTwoBit, and related programs from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
32     </p>
33     </body>
34     </html>

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