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1. Open BAM file.
2. Zoom in on the gene or region of interest.
3. Click Load Data.

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Soft-clipping is enabled by default in IGB, with the soft-clipped section of the read displayed in gray.

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1. Right-click the reads track label.
2. Select Configure soft-clip.

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Options for viewing soft-clipping include:

1. Show as default color - Soft-clipping shows as a default gray.
2. Show as custom color... - Using a color picker, soft-clipping shows as selected color.
3. Show as bases - Soft-clipping shows as Residue Colors.
4. Hide soft-clipping - Soft-clipping is hidden.

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Track Operations and Soft-clipping

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• Depth Graph (All) and Depth Graph (Start) ignore the soft-clipped parts of reads.
• Mismatch Graph and Mismatch Pileup Graph include the soft-clipped parts of reads.

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