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Objective: Validate that soft-clipping can be hidden and customized using the right-click menu of a bam track, as shown below:
Download Leaf1.small.aligned.sorted.softClipped.bam and Leaf1.small.aligned.sorted.softClipped.bam.bai
Open Leaf1.small.aligned.sorted.softClipped.bam and go to:
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Add the smoke test Data Provider to IGB using the following URL: https://quickload-testing.s3.amazonaws.com/smokeTestingQuickload/
- Open: Bam - PacBio with softclipping
- Navigate to: chr1:9,971-10,034
- Click Load Sequence to load sequence data, click Load Data to load data into it.
Ensure that loading data looks like this (you may need to optimize stack height set at 10, reads may be organized randomly):
- mac
- linux
- windows
Validate that the 'Configure soft-clip' submenu of the bam track right-click menu has 'Show as default color' selected.
- mac
- linux
- windows
Right-click on the bam track and select:
Configure soft-clip -> Show as custom color
A color
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picker should appear. Select a color (the example below selected red).
Ensure your view is as below, with the color you chose correctly applied
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:
- mac
- linux
- windows
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Right-click on the bam track and select:
Configure soft-clip -> Show as bases
Ensure your view is as below:
- mac
- linux
- windows
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Right-click on the bam track and select:
Configure soft-clip -> Hide softclipping
Ensure your view is as below:
- mac
- linux
- windows
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To test track operations are working correctly for soft-clipped data, right-click on the bam track and select:
- Track Operations > Depth Graph (All)
- Track Operations > Depth Graph (Start)
- Track Operations > Mismatch Graph
- Track Operations > Mismatch Pileup Graph
- Collapse
Ensure your view is as below:
- mac
- linux
- windows
