The Parameters Tab is organized as three sub-tabs: Input, Computation and Output (Figure 56). The input parameters that can be specified are different for the Genomic and cDNA sequence types. Each sequence type will have its own set of parameters under the project Input sub-tab.

For a new project, the mapping parameters are initially set to their defaults, as shown. If an invalid value is entered into any of these fields, an error indicator (red “X”) appears in the lower left corner of the field as well as on the tab heading, and the “Not ready for analysis” warning in the upper right hand corner of the screen. Pausing the mouse over the error indicator reveals a tooltip indicating the allowed values for the parameter (see section 2.14).