...

1. Click on a circular data node under the Analyses tab and expand the Pipelines section from the menu on the right (Figure 1). The context-sensitive menu (see Creating and Analyzing a Project) will only display pipelines that can be applied to the data type of the selected data node
    

   Numbered figure captions
   SubtitleText Loading a pipeline. In this example, the context-sensitive menu is showing all pipelines that can be applied to Aligned reads AnchorName Pipeline loading

2. Click on the pipeline name from the menu. Note that hovering the mouse over the pipeline name will show the description (if one was added) in a pop-out balloon (Figure 1)
    

3. If further settings need to be specified for any of the tasks, you will be redirected to a task-specific page. For example, if the chosen pipeline includes a STAR alignment task, you need to specify the species and STAR aligner index (Figure 2). Other tasks that require additional settings include Quantification to annotation model, Differential gene expression, Variant detection and others. For each task, specify the requested settings and click Next. Other task settings that were specified when the pipeline was saved (e.g. alignment parameters) will be applied automatically.
    

...