The getting started table
When no data has been opened for viewing, a table is visible in the View Area of the Workbench. This table provides links to sections of the application based user manual, and is thus a simple and fast way to access information about using the CLC Cancer Research Workbench.Currently CLC Cancer Research Workbench can be used to analyze DNA sequencing data. Analysis of RNA sequencing data is planned for a future release.
In this section, we take a closer look at the table in the viewing area (figure 2.2).
Figure 2.2: The table in the Cancer Research Workbench, visible when no datasets have been opened for viewing, provides links so that you can quickly navigate to relevant sections of the application based manual. To the right hand side of the table, the "Getting Started" and "Explore and Learn" areas provide links to more general information resources that you may find useful.
Summary stages in data analysis are listed at the left side of the table: Data Preparation, Data Analysis, Interpretation, and Data Analysis and Interpretation. Click on the text in the table to open the relevant section in the application based manual.
The recommended way to use the table is to start at the top and click on one of the "Whole genome", "Whole exome", or "Targeted" tabs found under the big "DNA" label if you are working on DNA-seq data. This acts to select the relevant application area. This done, when you click on a link within the "DNA" section of the table, you will be directed to the section in the application based manual about that topic, for example, "Annotate Variants" that applies to that particular application area, for example, "Whole genome analysis". Likewise, if you work on RNA-seq data, you can find relevant manual entries with the links provided under the big "RNA" label.
To the right side of the table is a box with two sections; "Getting started" and "Explore and learn". The "Getting started" area contains links to: the Tutorials (http://clccancer.com/tutorials/), Full-length application based manual (PDF), and Full-length reference manual (PDF) (http://clccancer.com/software/#downloads). The "Explore and Learn" section provides links to different sections of the application based manual as well as a link to a web page where you can download example data.
Finally, the Download example data provides links to two different example data sets. This is described in Import of example data