Exon identification and discovery

Clicking Next will show the dialog in figure 27.7.

Image mrna_seq_step3
Figure 27.7: Exon identification and discovery.

The choice between Prokaryote and Eukaryote is basically a matter of telling the Workbench whether you have introns in your reference. In order to select Eukaryote, you need to have reference sequences with annotations of the type mRNA (this is the way the Workbench expects exons to be defined - see in the introduction).

Here you can specify the settings for discovering novel exons. The mapping will be performed against the entire gene, and by analyzing the reads located between known exons, the CLC Genomics Workbench is able to report new exons. A new exon has to fulfill the parameters you set:

Figure 27.8 shows an example of a putative exon.

Image putative_exon
Figure 27.8: A putative exon has been identified.