Create library from bait group search results

If you have existing bait groups, and you want to create a library with them, you can use the method described in this topic. You can also use this method to create libraries with the new bait groups that you create in eArray. You first use eArray's bait group Search or Browse tools to find and select one or more bait groups to include in your library. You then define design parameters and create the library.

You can also use a wizard that leads you through this process. See Create library from existing bait groups (wizard).

Search or Browse for the desired bait group(s). If you intend to include multiple bait groups in your library, you do not have to retrieve all of them at once — you can add additional bait groups later in the process.

The Search Results pane lists the bait groups that match your search criteria.
Select the desired bait groups. Use the following as a guide:
- To select a bait group, mark the check box next to its name.
- To go to another page of bait groups, click one of the Pages links.
- You can select more than one bait group. eArray remembers your selections as you go from page to page.
- To select all of the bait groups on a page, mark the check box in the column heading row.
Click Create Library.

A species selection page appears.
In Select Species, select the desired species.

Species is required. eArray uses the species to select the appropriate Agilent control baits for your library, and also as a search key for library searches.
Click Next.

The Create Library page appears. Your selected bait groups appear at the bottom of the page, in the Bait Group Details tab.
Set library parameters in the Create Library pane. Parameters are required, unless otherwise indicated.

Parameter	Instructions/Details
Library Name	Type a name for the library. eArray uses this name as one of the search keys for libraries, and as a way to refer to it in search results, lists, and the like.
Species	(Read-only) The species that you selected previously in the library creation process
Length	eArray supports a bait length of 120 nucleotides. All baits in a library must have the same length. When you select a length, eArray automatically sets the library size. For the SureSelect Target Enrichment application type, eArray also selects the appropriate control grid.
Status	(Read-only) eArray initially creates new libraries with a status of Draft.
Description	(Optional) Type a brief description for the library.
Library Size	(Read-only) eArray supports a library size of 1 X 55K, which can accommodate up to 57,750 baits, including any required Agilent quality control baits. For the SureSelect Target Enrichment application type, click Show Details to see additional information about available features and the control grid that will be applied. In addition, for this application type, eArray automatically creates a library set when you design a library that contains more than 57,750 baits. See the note at the end of Step 7.
Folder	Select a location for your new library. The folders to which you have access appear in the list.
Comments	(Optional) Type comments to include with the library.
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. To select an alternate control grid, if one is available, click . A window opens where you can select the desired alternate control grid. Agilent has two control grids: Hs and Generic. If you select H. sapiens as the species, eArray automatically selects the Hs control grid. Otherwise eArray selects the Generic control grid. These small groups do not affect your capture and are for Agilent QC purposes. For the bait groups that you add, generally users designate all of them with a control type of biological. If you have a control group planned (and you want to, for example, hybridize spiked-in DNA to those baits), then you could designate the group with a control type of Positive. This designation does not have any special effect on the synthesis of the library. Control baits are not listed in the BED file.
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, specify the following: Name – Type a name for the attachment. This name becomes the link 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 search keywords to associate with the library, separated by commas. Keywords can help you search for the library.

Note the calculated values that appear at the bottom of the pane, which track library statistics as you add or remove bait groups. See Calculated library statistics for a description of these values.

In the Bait Group Details tab, make changes to the bait groups in the library. These tasks are available:

Task	Instructions/Details
Add bait group(s)	To add bait group(s) to your library: Click Add. A bait group selection page appears. In Bait Group Name, type all or part of the name of a bait group, then click Search. To return a list of all available bait groups, leave Bait Group Name empty. A list of bait groups appears. Do any of the following to navigate the list of bait groups. To go to another page of results, click one of the Pages links. To sort the list based on any column, click the heading of the desired column. To reverse the order of the items, click the column heading again. To limit the list to a specific folder, select the desired folder in Folder, then click Filter. Click the name of the desired bait group to select it. You can select more than one bait group on a page. Click Add. eArray transfers the selected bait group(s) to the Selected Bait Group list. Do any of the following to change the Selected Bait Group list: Add another bait group. Do another bait group search. You can add bait groups from multiple searches. Add all of the bait groups visible on a page — Click Add All. Start over — Click Remove All. Remove a bait group — Select the desired bait group, then click Remove. Click Done. eArray adds the selected bait group(s) to your library. To add additional bait groups to the library, click Add again.
View a bait group	In the Bait Group Name column, the names of bait groups in the library appear as links. Click the desired link to view details about the bait group. The View Bait Group page appears in a new window. For details about this page, see View bait group.
Remove bait group	To remove a bait group from the library: In the Select column, mark the check box next to the name of the bait group that you want to remove. Click Remove.
Change number of copies of bait group	In the Replicate column, next to the desired bait group, type the number of copies of the bait group you want to include in the library. Note: • eArray only lets you change the Replicate values for bait groups if you select Maximize capacity in Agilent Recommended Bait Boosting. Otherwise, eArray enforces a Replicate value of 1 for all bait groups in the library. • eArray replicates the required Agilent control bait group the same number of times as your least-replicated bait group. • eArray automatically includes as many complete sets of baits as will fit in the available space in the library. Example: Your library contains 12,000 baits, including the required Agilent control baits. The capacity of the 1 X 55K library format is 57,750 baits. eArray includes four complete sets of baits in your library (12,000 x 4 = 48,000 baits). Five complete sets would have exceeded the capacity of the library format (12,000 x 5 = 60,000 baits).
Change bait boosting preference	Bait boosting increases the representation of "orphan" and GC-rich baits within the library by an Agilent-defined factor. Agilent applies bait boosting to libraries by default. More info about bait boosting To make genomic fragment pull-down more consistent, Agilent increases the number of copies of both "orphan" and GC-rich baits in Agilent Catalog bait libraries. This process, called bait boosting, is also applied by default to custom libraries that you create in eArray. An orphan bait has no immediate neighbors in the genome within 1 bp on either side of the bait. This can occur when baits are tiled to very short regions, or when repeat or other regions are avoided during the tiling process and one or more short, isolated target regions are created. A GC-rich bait has a GC content of more than 65%. Both orphan and GC-rich baits produce less effective genomic fragment pull-down than other types of baits. Note: Bait boosting can be removed or applied when you create, edit, or review a library. Changes to bait boosting can only be made to libraries with a status of Draft or Review. . To change the bait boosting preference for the library In Agilent Recommended Boosting, select one of these options: Maximize Capacity – eArray applies no bait boosting to the library. This option lets you include the greatest number of user-defined baits in the library. Balanced – eArray replicates any orphan or GC-rich baits present in your library by an Agilent-defined factor, potentially improving the library's capture of genomic fragments. This option uses a greater number of the available baits in the library than the Maximize Capacity option, but it uses fewer baits than the Maximize Performance option. Also, if you select this option, eArray enforces a Replicate value of 1 for all bait groups in the library. Maximize Performance – To maximize the library's capture of genomic fragments, eArray replicates any orphan or GC-rich baits based on a sliding scale that reflects the boosting in Agilent’s catalog exome libraries. Baits with a higher GC content are replicated by a higher factor. This option can result in much higher levels of bait boosting than the Balanced option and, as a result, it uses the greatest number of the available baits in the library. Because the Maximize Performance option significantly boosts all GC-rich baits, Agilent does not recommend this option for libraries that cover non-coding regions with an atypically high GC content. A dialog box asks if you are sure you want to change your boosting preference. Click OK. Under Library Statistics, the value in Number of Available Features changes accordingly.

Note: (SureSelect Target Enrichment application type only) Currently, eArray supports the 1 X 55K library size, which can accommodate up to 57,750 baits. If you design a custom library that contains more than 57,750 baits, eArray automatically creates a library set, which distributes the requested baits evenly among multiple libraries. Library sets are handled as a single entity. You cannot separately work with or order the individual libraries in a library set. For details, see Library sets.

When a library set is needed to accommodate all of the requested baits in the library, eArray automatically marks the Enable Library Set check box. A dialog box tells you that multiple libraries are needed to cover the design. If you do not want to create a library set, you can remove bait groups from the library or decrease the number of copies of one or more bait groups until the library contains 57,750 baits or fewer.

eArray automatically enables and disables library sets as needed. You cannot manually mark or clear the Enable Library Set check box.

Click Create.

eArray saves your new library in the folder you selected with a status of Draft (or Review, if you created the library in a collaboration). A success message appears.
Click Close.

The Edit Library page appears.
Check the parameters and content of your library, and edit them if needed.

At this point you can also change the status of the library.

To submit a library to Agilent Manufacturing, you must first assign the library a status of Complete. In collaborations, you assign the library a status of Locking — when all collaboration leads approve locking, the status of the library changes to Complete. You then submit the library, after which you can request a quote or buy it from the Agilent Online Store.
Click Save.

eArray saves the edited library to the folder that you selected.