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:

1. 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/
2. Open the H_Sapiens_Dec_2013 genome.
3. In the Available Data panel, add the Bam - PacBio with softclipping data from your newly added Quickload.
4. Navigate to: chr1:9,971-10,034
5. Click Load Sequence to load sequence data, then click Load Data to load data into it.

• Loading data looks like this (stack height set at 10, reads may be organized randomly):

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• windows

• The Configure soft-clip submenu of the bam track right-click menu has Show as default color selected.

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• windows

1. Right-click on the bam track and select: Configure soft-clip -> Show as custom color.
2. Choose a red color from the color picker.

• Your IGB looks like the above image.

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• windows

Right-click on the bam track and select: Configure soft-clip -> Show as bases.

• Your IGB looks like the above image.

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• windows

Right-click on the bam track and select: Configure soft-clip -> Hide softclipping.

• Your IGB looks like the above image.

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• linux
• windows

To test track operations are working correctly for soft-clipped data, right-click on the bam track and select the following:

1. Track Operations > Depth Graph (All)
2. Track Operations > Depth Graph (Start)
3. Track Operations > Mismatch Graph
4. Track Operations > Mismatch Pileup Graph
5. Collapse

• Your IGB looks like the above image.

• mac
• linux
• windows