HomeCLC software: Important notificationsIssues affecting only versions of products released prior to June 2017Tracks in some track lists replaced by empty area when zooming or scrolling in Genomics WB 6.5 and 6.5.1

3.17. Tracks in some track lists replaced by empty area when zooming or scrolling in Genomics WB 6.5 and 6.5.1

This issue is related only to visualizing track lists and variant tracks when the viewing options for insertions are active. The issue and the work around do not affect the underlying data or any downstream analyses.

This issue affects users of  the Genomics Workbench 6.5 and 6.5.1, working with

  • tracklists containing two or more read mappings and/or
  • tracklists containing a read mapping and variant tracks, where viewing options associated with insertions in variant tracks have been turned on

When working with a single variant track, the same underlying problem causes variants to disappear from the view if viewing settings related to insertions are turned on.

This issue was fixed in CLC Genomics Workbench 6.5.2, released in January, 2014.

 

The tracklist viewing issue in detail

When working with a track list that contains two or more read mappings, one can end up being presented with a blank, grey area instead of tracks when zooming in, or scrolling back and forth along the mapping when zoomed partially or fully in.  The image below shows what one might see when zoomed fully out (left) and what one sometimes sees after zooming and scrolling (right).

The problem is related to the visualization of insertions in read mappings in track lists. Insertions are locations where an extra base (relative to the reference sequence) appears in a read or reads at a particular position in a mapping.

Work-around for CLC Genomics Workbench 6.5.0 and 6.5.1

  • Open up the view setting option for Read Mappings in the right hand pane.
  • Click on the small triangle to the left of the Read Mappings section to open up the relevant options list. 
  • Set the percentage for "Hide insertions below (%)" to 101.

 

The result of this change is that insertions relative to the reference in the mapping tracks are not shown. This does not affect your data or downstream analysis.

When working with individual variant tracks, please uncheck any boxes in the Insertions section of the viewing settings in the right hand pane of the Workbench to avoid any issues.

Knowledge Tags

This page was: Helpful | Not Helpful