Combine base and supplemental libraries (wizard)

For certain Agilent Catalog libraries, you can add baits for additional regions. To do this, you create a combined library. A combined library contains a base library and a supplemental library:

Base library – This library must be an Agilent Catalog library that is available in the currently selected application type, that has a Library Type of Base. Agilent Catalog libraries can be found in the AgilentCatalog folder.
- Note: You cannot select a custom library as a base library.
Supplemental library – This library must be a custom library with a status of Complete or Submitted, to which you have access in the currently selected application type. In addition, for the SureSelect Target Enrichment type, this library must have a Library Type of Supplemental, and contain baits that were created by the Bait Tiling wizard, with the desired base library selected in the Bait Tiling parameters.

You use the Create Combined Library wizard to create a combined library. Combined libraries have certain limitations. See the note at the end of this topic.

Before you create a combined library

Decide which Agilent Catalog library you want to use as the base library. To see the libraries that are available, you can browse the Agilent Catalog. If Base appears in the Library Type column in the list of libraries, the given library is available as a base library.
You must have a custom library (the supplemental library) that contains the baits that you want to add to the selected base library. The supplemental library can have up to 57,750 baits, including any required Agilent quality control baits. For the SureSelect Target Enrichment application type, the supplemental library must have a library type of Supplemental, and it must be created with the Bait Tiling wizard, with the desired base library selected in the Bait Tiling parameters.

To start the Combine Base and Supplemental Libraries wizard

Set the application type to SureSelect Target Enrichment or SureSelect RNA Enrichment.
In the Home tab of the Workspace tab, under Library Wizards, select Combine Base and Supplemental Libraries, then click Next.

The wizard appears in a new window. Initially, the first step of the wizard appears. The steps of the wizard are described in the sections below.
- Step 1 – Define Library
- Step 2 – Select Supplemental Library
- Step 3 – Layout Baits
- Step 4 – Create Library
- Note: For the SureSelect Target Enrichment application type, you can also create a combined library in a collaboration, and you can share a combined library from your individual user workspace in a new or existing collaboration.

Step 1 – Define Library

Enter the following library properties, as appropriate. All properties are required, except as noted.

Property	Instructions/Details
Library Category	(Read-only, SureSelect RNA Enrichment application type only) eArray supports RNA Capture libraries, which retrieve specific RNA species from a pool of RNAs.
Define Library
Library Name	Type a name for the combined library. eArray uses this name as a search key, and as a way to refer to it in search results, lists, and the like. The library name cannot have the same name as an existing Agilent Catalog library.
Base Library Name	Select the desired base library. The names of the Agilent Catalog libraries that are available as base libraries appear in the list. After you select a base library, eArray automatically sets the Control Grid, Length, and Species to those of the selected base library.
Folder	Select the desired destination folder for the combined library. The folders to which you have access appear in the list.
Length	(Read-only) The number of nucleotides in each bait in the combined library. All baits in the combined library have the same length. After you select a base library, eArray sets this property automatically.
Control Grid	(Read-only, SureSelect Target Enrichment Application type only) eArray automatically selects an appropriate control grid for the library. The name of the Agilent control grid appears as a link. To view details about the control grid, click the link.
Library Size	(Read-only) Currently, eArray supports bait libraries with a size of 1 X 55K, which can contain up to 57,750 baits, including the required Agilent quality control baits.
Species	(Read-only) The species associated with the baits in the library. After you select a base library, eArray automatically sets the species to that of the selected base library
Show Other Details (These optional properties appear if you mark Show Other Details.)
Description	(Optional) Type a brief description of the combined library. This information is saved with the library.
Comments	(Optional) Type brief comments to be saved with the library.
Attachment	(Optional) Attachments are files or links that are related your library. Attached files can be up to 32 MB in size. To add one or more attachments, follow these steps: Click . A page appears in a new window. In the Attach pane, enter the following: Name – Type a name for the attachment. This name becomes the link that you click to access the attachment. Type – Select the desired type of attachment from the list. An attachment can be either a file or a URL. Locale – Select the appropriate locale from the list. eArray uses this option to select content that has been localized for your region, when it is available. File – (Available only if you selected File for the type of attachment) Click Browse. Select the desired attachment in the dialog box that appears, then click Open. URL – (Available only if you selected URL for the type of attachment) Type the full URL of the Internet resource, including the protocol specifier. For example, http://www.agilent.com. Click Add. The attachment appears in the Attachment Header List at the top of the window. A success message appears. Click Close. Add additional attachments, if desired. If you add an attachment in error, select the check box next to its name in the Attachment Header List, then click Remove. Click Done. The window closes. The names of your attachments appear as links in Attachment.
Keywords	(Optional) Type a keyword, or multiple keywords separated by commas. Keywords can make your library easier to find in a library search, or when you browse libraries by category.

Click Next.

The next step of the wizard appears.

Step 2 – Select Supplemental Library

In this step of the wizard, you select a supplemental library to add to the selected base library. Under Select Supplemental Library, in the Search Results pane, a list of available supplemental libraries appears. Supplemental libraries are limited to custom libraries with a status of Complete or Submitted. For the SureSelect Target Enrichment application type, the available supplemental libraries are further limited to those that were created using the Bait Tiling wizard, with the desired base library selected in the Bait Tiling parameters.

Mark the desired supplemental library. You can select one supplemental library.
Click Next.

The next step of the wizard appears.

Step 3 – Layout Baits

In this step of the wizard, you confirm your selections of the base and supplemental libraries to be included in the combined library.

Inspect the details that appear in this step of the wizard. All details are read-only, and are described in the table below.

Detail	Description
Base Library Details
Name	The name of the base library that will be included in the combined library. A combined library contains exactly one base library.
ELID	The Agilent ID number of the selected base library. To see more information about the selected base library, click the ELID. The View Library page appears in a new window.
Folder	The location of the base library. Currently, base libraries are always found in the AgilentCatalog folder.
Supplemental Library Details
Name	The name of the supplemental library that will be included in the combined library. You include one supplemental library in a combined library.
ELID	(Appears if the supplemental library has a status of Complete or Submitted) The Agilent ID number of the selected supplemental library. To see more information about the selected supplemental library, click the ELID. The View Library page appears in a new window.
Folder	The location of the supplemental library.

If you need to change your selection of supplemental library, click Back. Otherwise, click Next.

The next step of the wizard appears.

Step 4 – Create Library

In this step of the wizard, you select a status for the combined library, and create the library.

Select one of these options:
- Complete – The library will be saved with a status of Complete to the location that you selected. Libraries with this status cannot be edited. Later, you can submit the library to Agilent Manufacturing and subsequently request a quote.
- Submitted – The library will be saved with a status of Submitted to the location that you selected. Libraries with this status cannot be edited or deleted. In addition, eArray submits the library to Agilent Manufacturing, which makes the library available for price quotes. You can also order the library from the Agilent Online Store through eArray.
Do one of the following:
- If you selected a status of Complete, follow these steps:
- 1. Click Save.
    A message tells you that the combined library has been successfully created.
  2. Click Close.
    A message tells you that the library was successfully created.
- If you selected a status of Submitted, follow these steps:
- 1. Click Design Checklist.
    A design checklist appears.
  2. Read and mark all of the items on the checklist, then click Done.
  3. Click Save.
    eArray saves the combined library to the location that you selected, and also submits the library to Agilent Manufacturing.
    A message tells you that the combined library was successfully created.
Click Close.

A message tells you that the library was successfully created.
Click Close.

A message tells you that a file write is in progress.
Click Close.

The View Library page appears in a new window with information about the new combined library.
Note:
• Combined libraries cannot be copied.

• If you submit a combined library, the system automatically saves the associated supplemental library with a status of Submitted.

• Bait boosting cannot be applied to a combined library. However, since the base library in a combined library is always an Agilent Catalog library, bait boosting has already been applied to the base library. Also, when you create a supplemental library for inclusion in a combined library, you can apply bait boosting to the supplemental library.