4.2. What is the difference between stand-alone objects and tracks?
The CLC Workbenches and Servers use two different object types, called Tracks and Stand-alone objects.
A key difference between a Stand-alone and Track-based sequence object is that a Stand-alone sequence contains all information relevant to that sequence in a single object. This includes any annotations as well as the sequence information itself.
In contrast, a Track-format object for a sequence contains very little information apart from the sequence itself. Annotations associated with that sequence are held in separate tracks. For example, you might have a Track for the Gene annotations, a Track for the CDS annotations, and etc. This provides greater flexibility in that you can view sets of Tracks in Track Lists, and thus can easily view together particular sets of annotations, or other information (e.g. Reads Tracks, Variant Tracks, etc.), at any given time.
Tracks are particularly useful when working with resequencing projects where several samples are analyzed against the same reference sequence. Therefore, this object type is used for RNA-Seq, Epigenomics and Resequencing.
Tracks are described in more detail in the following manual page:
Stand-alone objects are on the other hand more flexible as they are not tied to a common reference and are used for Sanger sequence analysis, cloning, de novo assembly, genome finishing, metagenomics, etc.
Based on the nature of the analysis that our different Workbenches can be used for, Biomedical Workbench primarily works using Tracks, CLC Genomics Workbench uses both Tracks and Stand-alone objects, while the Main Workbench only uses Stand-alone objects.
In CLC Genomics Workbench, objects can be converted to Tracks or from Tracks using tools in the Track Tools section of the Workbench Toolbox.
The simplest way to determine if an object is a Track or a Stand-alone object is by looking at the icon for that object in the Navigation Area of your Workbench. The icons for track-based objects include a small blue bar graph at the bottom. Therefore, objects without these blue bars are not in track format.
The following images include examples of Track and Stand-alone data objects.
Example of a Track list:
Example of a Stand-alone mapping viewed along with an annotated variant table: