Create library from existing bait groups (wizard)

Parameter

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.

Species

Select the species that best represents the content of the library that you want to create.

Parameter

Instructions/Details

Library Type

Select between creating a Normal library and a Supplemental library. A supplemental library is intended to be paired with an Agilent catalog library to create a combined library. Supplemental libraries can contain up to 57,750 baits, including the required Agilent quality control baits. A normal library is not paired with an Agilent catalog library, but if desired, it can later be used to create a combined library using the Combine Libraries wizard.

If you select Supplemental as the library type, you need to then make additional selections:

• Base Library Name drop-down list:Select the Agilent catalog library that you want to pair with the supplemental library when you later create the combined library.

• Ignore intervals already covered in base library check box: Mark the box if you want to skip adding baits to the supplemental library that overlap with genomic regions already covered by the chosen catalog library.

Library 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.

Length

eArray supports a bait length of 120 nucleotides. All baits in a library have the same length.

Folder

Select a location for your new library. The folders to which you have access appear in the list.

Species

(Read-only) Reflects the species that you selected in the previous step of the wizard.

Library Size

(Read-only) Currently, eArray supports a library size of 1 X 55K, which can accommodate up to 57,750 baits, including the 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.

Control Grid

(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.

Show Other Library Details (The properties below appear if you mark Show Other Library Details.)

Description

(Optional) Type a brief description for the library.

Keywords

(Optional) Type search keywords to associate with the library, separated by commas. Keywords can help you search for 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:

1. Click .
   A page appears in a new window.

2. In the Attach pane, specify 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.

3. Click Add.
   The attachment appears in the Attachment Header List at the top of the window. A success message appears.

4. Click Close.

5. 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.

6. Click Done.
   The window closes. The names of your attachments appear as links in Attachment.

Comments

(Optional) Type comments to include with the library.

Task

Instructions/Details

Bait Group Details

Add bait
group(s)

To add bait group(s) to your library:

1. Click Add.
   A bait group selection page appears.

2. 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.

3. Do any of the following to navigate through the list of bait groups.

1. • To navigate among multiple pages of results, use the Pages links.

   • To sort the list based on any column, click the heading of the desired column. To reverse the order of the sort, click the column heading again.

   • To limit the list to a specific folder, select the desired folder in Folder, then click Filter.

4. Click the name of the desired bait group to select it. You can select more than one bait group on a page.

5. Click Add.
   eArray transfers the selected bait group(s) to the Selected Bait Group list.

6. Do any of the following to change the Selected Bait Group list:

4. • 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.

7. Click Done.
   The selected bait groups appear under Bait Group Name in the main window of the wizard.
   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:

1. Mark the check box next to the name of the bait group that you want to remove.

2. 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 change the bait boosting preference for the library

1. 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.

2. Click OK.
   Under Library Statistics, the value in Number of Available Features changes accordingly.