Edit library

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.

Status

Select the desired status.

• Important: The status of a library follows a defined one-way order. Once you advance the library to the next status, and save it, you cannot set it back to a previous status.

Description

(Optional) Type a brief description for the library.

Library Size

(Read-only) Currently, eArray supports a library size of 1 X 55K, which can accommodate up to 57,750 baits. Click Show Details to see additional information about available features and the control grid that will be applied.

For the SureSelect Target Enrichment application type, if you design a library that has more than 57,750 baits, eArray automatically creates a library set, which can accommodate a larger number of baits over multiple libraries. For details see Library sets.

Folder

Select a location for the 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) The name of the currently selected 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 associated with your library. Attached files can be up to 32 MB in size.

To add one or more attachments

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 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.
   To remove an attachment, mark the check box next to its name in the Attachment Header List, then click Remove.
   You can also edit the attachments to a library. In the Action column, next to the attachment you want to edit, click Edit. When you finish making changes, click Save.

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

To remove an attachment

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

2. Under Attachment Header List, mark the check box next to the attachment you want to remove.

3. Click Remove.
   A message informs you that your attachment has been removed successfully.

4. Click Close.

5. Under Attachment Header List, click Done.
   eArray returns you to the Edit Library page, where you can continue your review.

Keywords

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

Task

Instructions/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 the list of bait groups.

1. • 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.

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 in the Bait Group Details tab.
   To add additional bait groups to the library, click Add again.

8. Note: All baits in a library must have the same length.

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. In the Select column, 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 desired number of copies.

• 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 – No bait boosting is applied to the library. This option can let you include a greater number of user-defined baits in the library.

   • Maximize performance – If your library contains any orphan or GC-rich baits, eArray replicates these baits by an Agilent-defined factor. This option can improve genomic fragment pull-down, but it uses a greater number of the available features in the library. Also, if you select this option, eArray enforces a Replicate value of 1 for all bait groups in the library.

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.

View library statistics

Calculated statistics about the library appear in the middle of the page. As you edit the library, these statistics can help you monitor how full the library becomes. For details, see Calculated library statistics.