Introduction

Soft-clipping of reads is done during alignment to mask portions of the reads that do not align to the reference sequence.

Visualizing soft-clipping can be useful for identifying contaminating adapter sequences or detecting structural variants.

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 your own data with soft-clipping in IGB:

Add your BAM file to IGB.
Zoom in on the gene or region of interest.
Click Load Data.

To view the example soft-clipping data in the images below:

Open the human genome (H_sapiens_Dec_2013) in IGB.
Navigate to: chr1:3,320-26,768
Hide the RefSeq Curated annotation track by right-clicking and selecting Hide.
Download the two files below:
1. pacBio.bam
2. pacBio.bam.bai
In IGB, select File > Open File...
Select the pacBio.bam file and click Open.
Click Load Sequence to load sequence data.
Click Load Data to load data into it.

IGB User's Guide > Soft-clipped reads > 1-softClipping-callout.png

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.

IGB User's Guide > Soft-clipped reads > 2-softClipping-callout.png

Options for viewing soft-clipping include:

Show as default color - Soft-clipping shows as a 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.

IGB User's Guide > Soft-clipped reads > 3-softClipping-callout.png

IGB User's Guide > Soft-clipped reads > 4-softClipping-callout.png

IGB User's Guide > Soft-clipped reads > 5-softClipping-callout.png

Note: When using the hide soft-clipping option, a line showing the full length of the read including the soft-clipped portion will appear.

To completely hide the soft-clipping portion of the read, use the Show as Custom Color soft-clip option, and select the same color as the background for the track.

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.

IGB User's Guide > Soft-clipped reads > 6-softClipping-callout.png

Data used in these examples is a subset taken from the Genome in a Bottle consortium (HG002 PacBio CCS 10kb):

Zook JM, Catoe D, McDaniel J, et al. Extensive sequencing of seven human genomes to characterize benchmark reference materials. Sci Data. 2016;3:160025. Published 2016 Jun 7. doi:10.1038/sdata.2016.25