Defining mapping options for RNA-Seq

When the reference has been defined, click Next and you are presented with the dialog shown in figure 28.5.

Image mrna_seq_step2b
Figure 28.5: Defining mapping parameters for RNA-Seq.

The mapping parameters are identical to those applying to Map Reads to Reference, as the underlying mapping is performed in the same way. For a description of the parameters, please see Mapping parameters.

For the estimation of paired reads distances, RNA-Seq uses the transcript level reference sequence information. This means that intronic regions are not included during this step - reflecting the true nature of the transcript on based on which the paired reads were produced.

In addition to the generic mapping parameters, two RNA-Seq specific parameters can be set: