Review library

 

After you create a library in your individual user workspace, eArray gives it a status of Draft. Subsequently, you can give it Review status, which lets other users make changes to it. In addition, eArray saves every reviewed version of the library. This topic describes how the owner of a library can place it in review, and how users can then review it. For the SureSelect Target Enrichment application type, you can also use the procedures in the topic to review a library set.

In a collaboration, a newly-created library has an initial status of Review. Collaboration members can review the library and make changes to it.

To place a library in review

You must be the owner of a library to place it in review. The library must have a status of Draft.

  1. Search or browse for the desired library.

    A list of libraries appears. To go to another page of results, click one of the Pages links. Also, you can filter the list of libraries to show only the ones with a status of Draft — Above the search results, in Status, select Draft, then click Filter.

  2. In the Actions column, next to the desired library, click Edit. You can only edit libraries that you own, and that have a status of Draft.

    The Edit Library page appears.

  3. In Status, select Review.

  4. Important: After you save the library with a status of Review, you cannot change the status back to Draft. Any additional edits must be part of the review process.

  1. Click Save.

    eArray makes the library available for review. A success message appears.

  2. Click Close.

    The Edit Library page remains in the main window. You can immediately make review changes.
     

To review a library

To review a library, you must have access privileges for it, and it must have a status of Review. The owner of the library, as well as other users, can review it as many times as needed.

  1. Search or browse for the desired library.

    A list of libraries appears. You can filter the list to show only libraries with a status of Review — At the top of the Search Results pane, in Status, select Review, then click Filter.

  2. In the Actions column, next to the desired library, click Review. You can only review a design/set that has been given a status of Review by its owner.

    The Edit Library page appears.

    eArray keeps all review versions of a library, each with its own version number. By default, eArray always sets the original version of the library as the "current" version, and uses it as the starting point for all reviews. Only the current version can be searched, browsed, or reviewed. If you are the owner of the library, you can select any version as the current one—follow these steps:

    1. Click the Version History tab.
      A list of all versions of the library appear.

    2. In the Current column, select the version of the library that you want to review.
      A dialog box appears.

    3. Click OK.
      A message informs you that the library version was successfully updated.

    4. Click Close.
       

  1. Change the following parameters, as desired. All parameters are required, unless indicated. The parameters on the page that are not described below are either calculated by eArray or are informational only, and cannot be edited.

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

(Available to the owner of the library or collaboration leads, read-only to other users) Select the desired status.

In your individual user workspace, you can keep the status as Review, or you can select a status of Complete. See Complete library.

In a collaboration workspace, you can keep the status as Review. If you are a collaboration lead, you can also select a status of Locking. See Lock library. After all leads approve locking, eArray automatically sets the status of the library to Complete.

  • 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.

Folder

(Available to the owner of the library or collaboration leads, read-only to other users) Select a location for the library. The folders to which you have access appear in the list.

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 plus_minus_icon.gif.
    A page appears in a new window.

  2. 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.

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

  2. Click Close.

  3. 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.

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

To remove an attachment

  1. Click plus_minus_icon.gif.
    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.

Description

(Optional) Type a brief description for the library.

Comments

(Optional) Type comments to include with the library.

Keywords

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

Library Size

(Read-only) Currently, eArray supports a library size of 1 X55K, 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.

Control Grid

 

(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 plus_minus_icon.gif. 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.

  1. In the Bait Group Details or Version History tabs, perform any of the following tasks.

Task

Instructions/Details

Bait Group Details tab

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.

    • 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.

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

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

  3. 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.

  1. Click Done. You may need to scroll down to see this button.
    The selected bait groups appear in the Bait Group Details tab.
    To add additional bait groups to the library, click Add again.

  2. Note:
    • Use the calculated statistics that appear in the middle of the page to monitor the size of the library. For more information on these statistics, see Calculated library statistics.

    • 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. Mark the check box next to the name of the bait group 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 – 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.

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

Version History tab

Place a different version of the library in review

(Available to the owner of the library or to collaboration leads) Each time a user saves a library that has a status of Review, eArray saves a copy of the library. Each new version of the library has a new, higher version number. By default, eArray always sets the original version of the library as the current version, and uses it as the starting point for all reviews. Only the current version can be searched, browsed, or reviewed. However, if you are the owner of the library, you can select any version as the current one.

  1. In the Version History tab, select the version of the library to make current.
    A dialog box appears.

  2. Click OK.
    A message tells you that the library version has been updated.

  3. Click Close.

    1. 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 can appear that 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.

  1. Click Save.

    eArray saves the reviewed library to the folder you selected.  Each time a reviewer saves a library, eArray creates a new version of it, assigns it a new version number, and saves a copy of it. eArray also dynamically generates a tab-delimited text (.tdt) file that anyone with access privileges for the library can download.

    You, and other users, can review the library as many times as desired the review process ends. In a collaboration, the review process ends when the collaboration leads lock the library. Outside of a collaboration, the review process ends when the owner of the library sets the status of the library to Complete.

A dialog box tells you that the library has been successfully updated.

  1. Click Close.

    eArray returns you to the Edit Library page, where you can continue to review the design.

See also

Edit library

Complete library

Submit library

Delete library