...

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. Soft

Visualizing 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

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 within IGB, first load a BAM filein IGB:

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

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

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

Image Removed 

Image Added

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

...

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

Image RemovedImage Added

Options for viewing soft-clipping include:

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

Image Added

Image Added

Image Added

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.

Image RemovedImage Added

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