Slime mold QuickLoad data directory

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 Loraine Lab) created all the files you see here using GFF files obtained in July 2010 from the dictyBase file Download section.

To access these data in Integrated Genome Browser, launch IGB (see: bioviz.org/igb) 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 The IGB User's Guide.)

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!

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.

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.

We gratefully acknowledge Siddhartha Basu of Northwestern University and the dictyBase Team for helping us set up this Dicty QuickLoad site. Thank you and we look forward to working with you in future!

Sincerely,
The Loraine Lab IGB team

 Name                         Last modified      Size  Description
 Parent Directory                                  -   
 all.bed                      19-Jul-2010 11:54  1.6M  Annotation file in BED format
 annots.xml                   19-Jul-2010 11:54  1.8K  Annotation file list
 D_discoideum_Ax4_May_2009.fa 22-Jul-2010 08:59   33M  Dictyostelium discoideum strain Ax4 May 2009 genome
 dictyBase_Curator.bed        19-Jul-2010 11:54  643K  Annotation file in BED format
 GenBank.bed                  19-Jul-2010 11:54  532   Annotation file in BED format
 geneID_reprediction.bed      19-Jul-2010 11:54  1.2K  Annotation file in BED format
 mod_chromInfo.txt            19-Jul-2010 11:54  137   Chromosome lengths and assembly information
 Sequencing_Center.bed        19-Jul-2010 11:54  965K  Annotation file in BED format
 Soderbom_group.bed           19-Jul-2010 11:54  4.9K  Annotation file in BED format
 tRNAscan-SE_analysis.bed     19-Jul-2010 11:54   26K  Annotation file in BED format