A supplemental library supplies additional baits that can be added to
a specific base library when you
create
a combined library. This help topic describes how to create a supplemental
library for the SureSelect Target Enrichment
application type. When you create a combined library within the SureSelect
RNA Enrichment application type, a supplemental library can be any custom
SureSelect RNA Enrichment library to which you have access.
When you create a supplemental library for the SureSelect Target Enrichment
application type, you first select an Agilent Catalog library as the base
library. Only certain Agilent Catalog libraries are available as base
libraries. eArray then uses Bait Tiling, and genomic intervals that you
enter, to create the baits in the supplemental library. For the Bait Tiling
job, eArray uses the same Bait Tiling parameters that were used in the
creation of the base library. Supplemental libraries have some important
limitations. See the note at the end of this
topic.
Before you create a supplemental 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 AgilentCatalog folder. If Base
appears in the Library Type column in the list of libraries, the given
library is available as a base library.
(Optional) Create a *.txt
file that contains a list of the genomic intervals to which you want
to design additional baits. Put one interval on each line. Use the
format illustrated in this example: chr17:12345678-12789011
To create a supplemental library
You use a wizard to create a supplemental library. Follow these steps
to start the wizard:
Set
the application type to SureSelect
Target Enrichment.
In the Home tab of the Workspace
tab, under Library Wizards, select Create
Supplemental Library by Bait Tiling, then click Next.
The Create Supplemental Library by Bait Tiling wizard appears. Initially,
the first step of the wizard appears. Each step of the wizard is described
separately, below.
Step
1 – Library Options
and Target Details
In this step of the wizard, you select a base library, and set up a
Bait Tiling job based on the Bait Tiling parameters that are defined for
the base library. For more information about Bait Tiling, see Bait
Tiling (SureSelect Target Enrichment).
Under Choose Base Library, in Library Name, select the desired
base library. The Agilent Catalog libraries that are available as
base libraries appear in the list.
eArray sets most of the parameters under Design Options, based on the
Bait Tiling parameters that are defined for the base library that
you selected.
Under Design Options, in Design
Job Name, type a name to identify the Bait Tiling job. All
other parameters under Design Options are read-only, and are set automatically.
Under Target
Details, enter information about the genomic intervals to be
tiled, and those to be avoided. These details appear:
Parameter |
Instructions/Details |
Species |
(Read-only) The species to which
baits will be designed. eArray automatically sets the species
based on the species that is defined for the selected base library. |
Genome
Build |
(Read-only) The genome build of
the species to which baits will be designed. eArray automatically
selects the genome build based on the genome build that is defined
for the base library. |
Genomic
Target Intervals |
Type the desired target intervals.
Use the format chrX:<start>-<end>. Separate multiple
intervals with pipe "|" characters.
Example:
chr21:1000000-1500000|chrY:2000000-2300000
Alternatively,
you can upload a list of intervals. Create the list as a *.txt
file with one interval per line. End each line with a new line
character. (In a word processor, press Enter
at the end of each line.) Then
follow these steps:
Next
to the Genomic Target Intervals box, click Upload.
A dialog box appears. Click
Browse.
A Choose File dialog box appears. Select
the desired file, then click Open.
The name of the file appears in the previous dialog box, in
File Name. Click
Upload File.
eArray uploads the list of intervals, and displays them in
pipe-separated format in the Genomic Target Intervals box. |
Avoided
Genomic Intervals |
Mark any of these options:
Avoid Standard Repeat Masked Regions
– eArray
excludes a standard set of repetitive genomic regions from
the Bait Tiling process. These are regions of the genome that
generally produce poor quality baits. This option is marked
by default. To see specific information about how standard
repeat regions are defined, click the Info
link next to this option. Avoid Custom Intervals – In the Bait Tiling process,
eArray excludes the genomic intervals that you enter in the
box. Use the format chrX:<start>-<end>. Separate
multiple intervals with pipe "|" characters.
Example: chr21:1000000-1500000|chr5:6200000-6400000
Alternatively, you can upload a list of intervals. Create the
list as a *.txt file with one interval per line. End each
line with a new line character. (In a word processor, press
Enter at the end of
each line.) Then follow these steps:
Next
to the Avoid Custom Intervals box, click Upload.
A dialog box appears. Click
Browse.
A Choose File dialog box appears. Select
the desired file, then click Open.
The name of the file appears in the previous dialog box,
in File Name. Click
Upload File.
eArray uploads the list of intervals, and displays them
in pipe-separated format in the Avoid Custom Intervals
box. |
Click Submit.
The next step of the wizard appears.
Step
2 – Upload Message
In this step of the wizard, a message tells you that your Bait Tiling
job has been submitted, and that you will receive an e-mail when the tiling
job is completed.
Read the message, then click
Close.
The wizard closes. Before you can continue with the wizard, you must
wait for eArray to complete the Bait Tiling job, which can take up
to one day or more. You can monitor the status of the job at the bottom
of the Library Wizards pane in the Home tab of the Workspace tab.
The job can have these statuses:
Status |
Description |
Bait
Tiling Submit |
The job has been submitted to Agilent,
but no action has been taken on it yet. |
Baits
Upload Processing |
The job has been submitted to Agilent,
and processing has begun. |
Baits
Uploaded |
The job has been completed by Agilent,
and the results are available for your use. |
ERROR |
The job has been submitted to Agilent,
but there are problems. You must resubmit your job. eArray
sends you an e-mail informing you of the error. This e-mail
can contain additional information about the error. |
When the job has a status of Baits Uploaded,
you can continue with the wizard.
Step
3 – Define Library
In this step of the wizard you define certain properties of the supplemental
library. Before you can continue with the wizard, the Bait Tiling job
that you submitted in the first two steps of the wizard must have a status
of Baits Uploaded.
Click the Workspace
tab, then click the Home tab.
The Home tab of your individual user workspace appears.
At the bottom of the Library Wizards
pane, next to the name of the Bait Tiling job that you submitted in
the previous steps of the wizard, in the Action column, click Continue.
The wizard reappears.
Under Define Library, enter the
desired properties of the library. The table below describes the properties
that appear. Some properties are set by the system, and cannot be
changed.
Property |
Instructions/Details |
Library
Name |
Type a name for the supplemental
library. The name that you use must be different from the name
of the base library. |
Base
Library Name |
(Read-only) The name of the base
library that you selected in the first step of the wizard. |
Folder |
Select a location for your new library.
The folders to which you have access appear in the list. |
Control
Grid |
(Read-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. |
Length |
(Read only) The number of nucleotides
in each bait in the library. This value is the same as the one
defined for the base library. |
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.
To see information
about the number of features and the available control grids for
the library, click Show Details. |
Keywords |
(Optional) Type search keywords
to associate with the library, separated by commas. Keywords can
help you search for the library. |
Species |
(Read-only) The species that is
associated with the baits in 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.
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, mark the check box next
to its name in the Attachment Header List, then click Remove. Click
Done.
The window closes. The names of the attachments appear as links
in Attachment. |
Click Next.
The next step of the wizard appears.
Step
4 – Layout Baits
In this step of the wizard, you view the content and statistics of the
supplemental library.
Inspect the information that appears
in this step of the wizard. All items are read-only. You cannot change
the bait content of the library.
Detail |
Description |
Bait
Group Details |
Bait
Group Name |
The name of the bait group that
contains the baits that were produced by the Bait Tiling job that
you submitted earlier in the wizard. To view the bait group in
greater detail, click its name. |
Control
Type |
The bait group in a supplemental
library always has a control type of biological. The control type
of a bait group has no effect on the composition of a library,
and is provided for user reference. |
Replicate |
For the bait group in a supplemental
library, this parameter is always set to 1.
Note: 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
been too many for the library format (12,000 x 5 = 60,000
baits). |
Library
Statistics |
Percentage
Filled |
The percentage of the total number
of features in the library that are occupied by baits. |
Number
of Available Features |
The number of unused features in
the library. These features do not contain baits. |
Total
number of Features |
The maximum total number of baits
that can be accommodated in the library. eArray currently supports
a library size of 1 X 55K, which accommodates up to 57,750 baits,
including the required Agilent quality control baits. |
Number
of User Controls |
eArray does not currently support
user control baits in supplemental libraries. Therefore, this
statistic is always 0. |
Number
of Agilent Controls |
The number of Agilent quality control
baits that are included in the combined library. |
Do one of the following:
If the Percentage of Features
Occupied is greater than 100%, or another item is unacceptable,
click Cancel. This ends
the wizard. You can start the wizard again, and enter different
tiling parameters.
Step
5 – Create Library
In this step of the wizard, you select a status for your new supplemental
library, and create the library.
Select one of these options:
Do one of the following:
Click Design
Checklist.
The design checklist for SureSelect Target Enrichment libraries
appears.
Read and mark all of the
items on the checklist, then click Done.
Click Save.
eArray saves the supplemental library to the location that
you selected, and also submits the library to Agilent Manufacturing.
A message tells you that you will receive an e-mail confirmation
that the library has been submitted to Agilent Manufacturing.
Click Close.
In either case, eArray creates your library
and saves it with the selected status. A message tells you that your library
was successfully created.
Click Close.
A message tells you that a file write is in progress.
Click Close.
eArray displays the details of the library on the View Library page.
For details about this page, see View library.
Note:
•
You can create any number of supplemental libraries based on a
given base library. However, in a combined
library, you can only include one supplemental library with
the base library.
•
A supplemental library is associated with a specific base library.
In a combined library, a given supplemental library can only be
included with the specific base library with which it is associated.
•
You can request
a quote for a combined library or purchase
it from the Agilent Online Store through eArray. The quote
(or order) includes both the base library and the associated supplemental
library. However, you can also request quotes for and order supplemental
libraries as separate entities. The quotation and ordering process
for supplemental libraries is the same as that for regular custom
libraries.
•
eArray saves supplemental libraries with a status of either Complete
or Submitted. Therefore, supplemental libraries cannot be edited.
•
eArray creates a bait group that contains the baits that were
designed to your input genomic intervals by the Bait Tiling process.
Because this bait group is saved with a status of Locked, you
cannot edit it. However, you can search or browse for the bait
group and use it as you would other bait groups with this status.
See Bait groups.
•
You cannot move or share a supplemental library.
•
You can create a supplemental library in your individual user
workspace, but you cannot create one in a collaboration.
See
also
Create
a combined library
Bait
Tiling (SureSelect Target Enrichment)