The functionality described in this topic is only available when you mark Show Advanced Options.

HaloPlex advanced wizard:

Finalize/Design Complete

In this step, you can review the Design Summary one last time before finalizing the design. If any of the probegroups in the design were created with the Tile Genes or Regions method, the target information for those probegroups is displayed in the Target Details table. This table lists the following information for each of the target identifiers that was used for tiling:

·        Target ID - the gene name, transcript ID, or genomic coordinates that you used to define the target

·        Interval - the bounds of the genomic coordinates where SureDesign mapped the target ID; includes any flanking sequences and UTRs that you selected as regions of interest when creating the design

·        Length - the total number of base pairs in the target regions

·        Coverage - the percentage of nucleotides in the target regions of the target ID that are covered by one or more probes in the design

·        # Regions - the number of target regions within the target.

·        # Good Coverage -  the number of regions within the target ID that have >90% coverage

When you are ready, click Finalize Design to finish the design creation process. Alternatively, if you want to make further edits to the design, click Back to return to the Add/Review content step.

After clicking Finalize Design, the wizard window updates to the Design Complete step, and provides the following information:

Use the action buttons at the bottom of the Finalize Design window to take further action on the design:

·        Click Order to open the Order dialog box, where you can add the design to your Agilent Genomics shopping cart or submit a request to receive a price quote.

·        Click Mark as Favorite to add the design to your list of favorites. The design will appear in the Designs: Recent and Favorites dashboard on the Home screen.

·        Click Download to download one or more design files, including a formatted PDF report that summarizes key information on the design, probes, targets, and the probe selection job.

·        Click BAM to submit a request to generate a simulated BAM file for the design. You will be e-mailed a link to download the file. This action is only available for advanced HaloPlex designs in which the probegroups are a subset of probes from the HaloPlex Exome Agilent Catalog design.

·        Click UCSC View to launch your internet browser to the UCSC Genome Browser page. The design's AllTracks.BED file is loaded in the browser. You may need to disable the pop-up blocker in your internet browser in order to use this feature.