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Soft-clipping of reads is done during alignment to mask the beginning or end of a read that does portions of the reads that do not align to the reference sequence. SoftVisualizing soft-clipping of reads can occur due to un-trimmed can be useful for identifying contaminating adapter sequences or detecting structural variationvariants.
How to view soft-clipping in IGB
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- Right-click the reads track label.
- Select Configure soft-clip.
Options for viewing soft-clipping include:
- Show as default color - softSoft-clipping shows as a default gray.
- Show as custom color... - using Using a color picker, soft-clipping shows as selected color.
- Show as bases - softSoft-clipping shows as Residue Colors.
- Hide soft-clipping - softSoft-clipping is hidden.
Track Operations and Soft-clipping
Track Operations behave differently when soft-clipping is present.
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