Page History

...

•   All Default DataProviders appear in the DataProviderManagementGui table

• • Observation:  The table matches the image belowlists several Quickload sites. (They may be different from those shown below.) 

•  Confirm the following species / genome versions are available 
  • Arabidopsis thaliana / A_thaliana_Jun2009
    • Observation: Available Data Tree appears with the following several sites (IgbQuickload, Pollen, and Cytokinin. (They may be different from those shown below.)
      • 
  • Homo Sapiens/ H_sapiens_Dec_2013
    • Available data sites include UCSC and IgbQuickloaddata should list some data sets. (They may vary from those shown below.)
      
      • 
    •  Important: Confirm that the Cytobands track is visible
      • 

•  Load a bed file, a bam file, a bedgraph file, and some sequence data to ensure basic file parsing from the data providers is working as expected. ( Important: Load these directly from by selecting the checkboxes in the Data Access Treefolder hierarchy, not from the urls). For an example URLs displayed in a Web browser. To get examples of each file type, go the the Arabidopsis thaliana June 2009 genome.  Under RNA-Seq / Pollen there are three folders.  several folders labeled by experiment code and with a human-friendly name. Within those folders, there are folders labeled Reads, Graph, and Junctions. The Reads folder has bam files.  The Graph folder has bedgraph files.  The Junctions folder has bed files.  Select one file from each folder, zoom in to show only several thousand bases, and Load Data.  Most RNA-Seq experiments have a similar structure, are several examples in RNA-Seq and IGB-Quickload.  Use the "Load Sequence" click Load Data button at the top right of the IGB window. Click the Load Sequence button to load sequence and zoom in to make sure you can see individual letter (A, C, T, G) under the coordinate axis. 
  •  Bed File
  •  Bam File
  •  Bedgraph File
  •  Load Sequence

...