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The functionality described in this
topic is only available when you mark Show
Advanced Options.
Add Content
In the Add Content step, you select a method for adding probes to the probegroup. The SureSelect probegroup wizard offers multiple methods for adding content, which are described in detail below.
Select Add Content Method
Select the method you want to use for adding probes to your design:
· Select Optimized Probes - (Only available for H. sapiens designs) Agilent recommends the "Select Optimized Probes" option when adding content based on target genes or regions. This method uses a machine learning algorithm to select high-quality probes that cover the desired targets. Probes are selected based on multiple metrics of quality including specificity, GC content, and entropy. Probe density will vary between 1x and 5x depending on target properties such as the uniqueness of the target sequence in the genome, GC content, and target size. Notably, the algorithm ensures that the probe set does not include orphan probes (i.e., probes with no adjacent or overlapping probes). After you define the targets and set the parameters, you submit the design to Agilent as a probe selection job. You are notified via e-mail when your job is complete. See Add Content > Select Optimized Probes for instructions.
· Design new probes by tiling genes or regions - With this method, SureDesign select probes by tiling across the user-specified targets at the selected density. It follows the same workflow as that used in the standard wizard, but with some additional probe selection parameters. After you define the targets and set the parameters, you submit the design to Agilent as a probe selection job. You are notified via e-mail when your job is complete. See Add Content > Tile Genes or Regions for instructions.
· Upload probes - This method allows you to upload probes that you designed with your own algorithms. See Add Content > Upload Probes for instructions.
· Select probes from an existing Design or
Probegroup - This method allows you to add probes by selecting
an existing probegroup or design (custom or Catalog) and then selecting
probes from that design/probegroup to include in the new probegroup. If
you choose this method, you must specify how you want to select the subset
of specific probes from the existing design/probegroup.
The two options to select the subset of probes are:
· Select probes for specific genes or regions - to select probes from the selected design or probegroup that cover specific genes or regions
· Select probes by Probe ID - to select probes from the selected design or probegroup that cover specific Probe IDs. You can find the Probe IDs for an existing design/probegroup in the associated Probes.txt file.
Once you have made a selection, click Next to continue.