How to run the Annotate from Reference tool

        Toolbox | Genome Finishing Module (Image finishing_tools_folder) | Annotate from Reference (Image contig_extender_16_n_p)

This opens the dialog shown in figure 14.4 where at least one Align Contigs result must be selected. Click Next.

Image annotate_from_reference_step1
Figure 14.4: Select Align Contigs results.

The next step in figure 14.5 allows you specify the following:

Image annotate_from_reference_step2
Figure 14.5: Specify parameters for deciding in which cases an annotation should be transferred.

Figure 14.6 shows the output options. They include generation of reports and tables containing information on the annotations that were transferred and those that were not. You can also add annotations to aligned contigs, and create contigs with annotations. Click Finish to transfer annotations.

Image annotate_from_reference_output_step
Figure 14.6: Output options for the Annotate from Reference tool.