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

SureSelect probegroup wizard:

Add Content

Select Probe Source

Select probes by Probe ID

Once you have completed the Select Probe Source step, you will be directed to the Select probes by probe ID screen, if you chose this workflow on the Add Content step.

Screen 1 - Probe IDs

Enter the probe IDs in the text box provided. You can type or paste the probe IDs directly into the text area, or click Upload to browse to a text file (*.txt) that lists the probe IDs (one per line). Click the Example hyperlink to open a new window displaying an example list of Probe IDs. The Probe IDs for an existing design are listed in the design's probes.txt file. See Download design files for information on how to download this file for a particular design.

Click Next to continue to Screen 2.

Screen 2 - Target Summary

The Target Summary screen indicates the number of probe IDs entered on Screen 1.

Click Next to continue to Screen 3.

Screen 3 - Selection Parameters

The drop-down list on this screen allows you to select an option for the boosting parameter.

SureDesign can boost the number of copies for any GC-rich probes in the new probegroup. Boosting these probes can potentially improve their ability to capture target genomic fragments.

In the Boosting drop-down list, select one of the options described below. The default option is Balanced.

·        Optimized Performance XT/XT2 – This option is available when the hybridization type is set to Overnight or Not Specified. This boosting algorithm is specifically optimized for the hybridization conditions in the SureSelect XT and XT2 library preparation protocols to deliver optimal sequencing uniformity and read depth across the full range of GC content percentages.

·        Optimized Performance XT HS/ XT HS2/ XT LI/ QXT - This option is available when the hybridization type is set to 90 minutes or Not specified. This boosting algorithm is specifically optimized for the hybridization conditions in the SureSelect XT HS, XT HS2, XT Low Input, and QXT library preparation protocols to deliver optimal sequencing uniformity and read depth across the full range of GC content percentages.

·        No Boosting - SureDesign does not boost GC-rich probes when this option is selected.

·        Same as Catalog Design - Appropriate for all SureSelect library preparation methods. SureDesign uses the same replication factor as that used for each probe in the Agilent Catalog source design. Note that this option is not available for all catalog designs.

When finished making a selection for boosting, you can submit the probegroup for probe selection.

To submit the probegroup for probe selection:

1. Click Begin Probe Selection.
   
   A message box opens indicating the e-mail address where Agilent will contact you when the probe selection job is complete. If desired, you can enter additional e-mail addresses into the provided field.

2. Click OK in the notification message to submit the probegroup to SureDesign.
   
   Your submission is placed in the SureDesign job queue to await probe selection.
   
   The wizard takes you to the Finalize screen. The Finalize page indicates that probegroup creation has been started. Click Close to exit the wizard.
   
   You receive an e-mail from Agilent SureDesign notifying you when your job is complete.