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<title>Slime mold QuickLoad data directory</title>
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<h2>
Slime mold QuickLoad data directory
</h2>
<p>
This directory contains annotation files for the slime mold
Dictyostelium discoideum strain Ax4 genome that was available as of
May, 2009. Ann Loraine (of the <a
 href="http://www.transvar.org">Loraine Lab</a>) created all the files
you see here using GFF files obtained in July 2010 from the <a
 href="http://www.dictybase.org/Downloads/"> dictyBase file Download
section</a>.
</p>
<p>
To access these data in Integrated Genome Browser, launch IGB (see: 
<a href="http://www.bioviz.org/igb">bioviz.org/igb</a>) and 
choose species Dictyostelium discoideum Ax4 and then genome version 
D_discoideum_Ax4_May_2009 in the Data Access Panel. 
(For documentation about IGB, see <a href="http://wiki.transvar.org/confluence/display/igbman/Home">The IGB User's Guide</a>.)
</p>
<p>
All the available data files you see in this directory
should appear in the Data Sources section of the Data Access panel. If you want to load
everything all at once into several tracks, choose ALL and then choose Load Mode
Whole Genome under the Load Mode section of the Data Access Panel. The Dicty genome is
a very manageable size, and so we highly recommend you load everything all at once!
</p>
<p>
To view genomic sequence, zoom in and click Load Sequence in View or Load All Sequence. The
latter will load all the sequence for the current chromsome. Since this genome is quite
small, we highly recommend the Load All Sequence option.
</p>
<p>
To load next-gen sequencing data from sorted, indexed BAM files, just click-drag them
from your desktop or a server into the IGB interface. The same goes for "bar" (tiling
array) files.
</p>
<p>
We gratefully acknowledge Siddhartha Basu of Northwestern University and 
<a href="http://www.dictybase.org/About_dictyBase/">the 
dictyBase Team</a> for helping us set up this Dicty QuickLoad site. Thank you
and we look forward to working with you in future!
</p>
<p>
Sincerely,<br/>
The Loraine Lab IGB team
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[ICO]NameLast modifiedSizeDescription
[PARENTDIR]Parent Directory  -  
[ ]tRNAscan-SE_analysis.bed2023-06-16 13:15 26KAnnotation or junction file
[TXT]genome.txt2023-06-16 13:15 137 Chromosome lengths and assembly information
[ ]geneID_reprediction.bed2023-06-16 13:15 1.1KAnnotation or junction file
[ ]dictyBase_Curator.bed2023-06-16 13:15 643KAnnotation or junction file
[ ]annots.xml2023-06-16 13:15 1.8KAnnotation and data file list
[ ]all.bed2023-06-16 13:15 1.6MAnnotation or junction file
[ ]Soderbom_group.bed2023-06-16 13:15 4.9KAnnotation or junction file
[ ]Sequencing_Center.bed2023-06-16 13:15 965KAnnotation or junction file
[ ]GenBank.bed2023-06-16 13:15 511 Annotation or junction file
[ ]D_discoideum_Ax4_May_2009.fa.gz2023-06-16 13:15 9.1MSlime mold
[ ]D_discoideum_Ax4_May_2009.2bit2023-06-16 13:15 8.2MSequence data in blat 2bit format
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