General Function Checklist
Objective: Validate that soft-clipping can be hidden and customized using the right-click menu of a bam track, as shown below:
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- In the Data Sources tab in Preferences, add the smoke test Data Provider to IGB using the following URL: https://quickload-testing.s3.amazonaws.com/smokeTestingQuickload/
- Open
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- the H_Sapiens_Dec_2013 genome.
- In the Available Data panel, add the Bam - PacBio with
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- softclipping data from your newly added Quickload.
- Navigate to: chr1:9,971-10,034
- Click Load Sequence
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- to load sequence data,
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- then click Load Data to load data into it.
Ensure that loading 
- Loading data looks like this (stack height set at 10, reads may be organized randomly):
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Validate that the '
- The Configure soft-clip
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- submenu of the bam track right-click menu has
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- Show as default color
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- selected.
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- Right-click on the bam track and select:
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- Configure soft-clip -> Show as custom color
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A color picker should appear. Select a color (the example below selected red).
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- .
- Choose a red color from the color picker.
- Your IGB looks like the above image.
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Right-click on the bam track and select:
Configure soft-clip -> Show as basesEnsure your view is as below:.
- Your IGB looks like the above image.
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Right-click on the bam track and select:
Configure soft-clip -> Hide softclippingEnsure your view is as below: .
- Your IGB looks like the above image.
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To test track operations are working correctly for soft-clipped data, right right-click on the bam track and select the following:
- Track Operations > Depth Graph (All)
- Track Operations > Depth Graph (Start)
- Track Operations > Mismatch Graph
- Track Operations > Mismatch Pileup Graph
- Collapse
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- Your IGB looks like the above image.
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- linux
- windows