Mapping settings

When the reference has been defined, click Next and you are presented with the dialog shown in figure 30.5.

Image mrna_seq_step2b
Figure 30.5: 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 introns are not included in the distance measurement. The paired distance measurement will only include transcript sequence, reflecting the true nature of the sequence on which the paired reads were produced.

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

Concept of hits and distinct places in the reference

The definition of a distinct place in the reference sequence is complicated. We are describing here example cases where the option "Genome annotated with genes and transcripts" is selected in the previous "Reference settings" step, meaning that reads are aligned to genes and transcripts.