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<title>Slime mold QuickLoad data directory</title> |
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Slime mold QuickLoad data directory |
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<p> |
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This directory contains annotation files for the slime mold |
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Dictyostelium discoideum strain Ax4 genome that was available as of |
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May, 2009. Ann Loraine (of the <a |
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href="http://www.transvar.org">Loraine Lab</a>) created all the files |
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you see here using GFF files obtained in July 2010 from the <a |
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href="http://www.dictybase.org/Downloads/"> dictyBase file Download |
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section</a>. |
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</p> |
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<p> |
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To access these data in Integrated Genome Browser, launch IGB (see: |
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<a href="http://www.bioviz.org/igb">bioviz.org/igb</a>) and |
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choose species Dictyostelium discoideum Ax4 and then genome version |
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D_discoideum_Ax4_May_2009 in the Data Access Panel. |
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(For documentation about IGB, see <a href="http://wiki.transvar.org/confluence/display/igbman/Home">The IGB User's Guide</a>.) |
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</p> |
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<p> |
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All the available data files you see in this directory |
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should appear in the Data Sources section of the Data Access panel. If you want to load |
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everything all at once into several tracks, choose ALL and then choose Load Mode |
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Whole Genome under the Load Mode section of the Data Access Panel. The Dicty genome is |
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a very manageable size, and so we highly recommend you load everything all at once! |
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</p> |
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<p> |
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To view genomic sequence, zoom in and click Load Sequence in View or Load All Sequence. The |
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latter will load all the sequence for the current chromsome. Since this genome is quite |
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small, we highly recommend the Load All Sequence option. |
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</p> |
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<p> |
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To load next-gen sequencing data from sorted, indexed BAM files, just click-drag them |
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from your desktop or a server into the IGB interface. The same goes for "bar" (tiling |
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array) files. |
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</p> |
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<p> |
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We gratefully acknowledge Siddhartha Basu of Northwestern University and |
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<a href="http://www.dictybase.org/About_dictyBase/">the |
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dictyBase Team</a> for helping us set up this Dicty QuickLoad site. Thank you |
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and we look forward to working with you in future! |
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</p> |
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<p> |
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Sincerely,<br/> |
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The Loraine Lab IGB team |
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</p> |
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</body> |
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</html> |
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