Introduction
Soft-clipping of reads is done during alignment to mask the beginning or end of a read that does not align to the reference sequence. Soft-clipping of reads can occur due to un-trimmed adapter sequences or structural variation.
How to view soft-clipping in IGB
Note: Soft-clipped sections of reads are not visible in versions of IGB prior to 9.1
To view soft-clipping within IGB, first load a BAM file:
- Open BAM file.
- Zoom in on the gene or region of interest.
- Click Load Data.
Soft-clipping is enabled by default in IGB, with the soft-clipped section of the read displayed in gray.
To configure the appearance of soft-clips:
- Right-click the reads track label
- Select Configure soft-clip
Options for viewing soft-clipping include:
- Show as default color - soft-clipping shows as default gray
- Show as custom color... - using a color picker, soft-clipping shows as selected color
- Show as bases - soft-clipping shows as Residue Colors
- Hide soft-clipping - soft-clipping is hidden
Track Operations and Soft-clipping
Track Operations behave differently when soft-clipping is present.
- 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.
