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- 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 by selecting the checkboxes in the Data Access folder hierarchy, not from URLs displayed in a Web browser. To get examples of each file type, go the the Arabidopsis thaliana June 2009 genome. Under RNA-Seq there are 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 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
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Bam File
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Bedgraph File
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Load Sequence
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Load a few tracks from the UCSC DAS data source. Note: The UCSC DAS data source is not activated by default - you need to activate it in the Data Sources tab of the Preference window. Once this data source is active, it should be visible on Human/Mouse species.
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Adding/Removing/Editing DataProviders
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- The quickload site shows up in the "Available Data" tree
- The data sets listed in the tree can be loaded
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Confirm restarting IGB does not cause the newly added site to be forgotten
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Ensure that the edit button in the Data Sources window opens a new window and allows a user to modify the data source URL or to choose a local folder. Note that default data sources cannot be modified.
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Ensure that data sources can be deleted using the Remove button in the Data Sources window
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Add a few "Secured" quickload sites and confirm they are working as expected
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username/password
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Navigate to the Arabidopsis thaliana Jun_2009 genome version
Confirm the two sites are listed the "Available Data" tree and data can be loaded from each site
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Confirm you were not prompted for a password for any site more than a single time per session
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Confirm restarting IGB does not cause the newly added sites to be forgotten
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Confirm that if you checked the "Save Password" option you are not prompted for your password again on restarting IGB
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