View details of a design

When you open the details window for a design, you see the complete information for the design and have access to tools that allow you to take actions on the design.

To open the details window: Locate the design of interest in the table on the Find Designs screen (see View and search for designs for instructions) or in the Designs: Recent and Favorites dashboard on the Home screen. Click directly on the design name. The details window opens for that design. (If the design is available for multiple genome builds, SureDesign will prompt you to select the desired genome build prior to opening the details window.)

The tables in this help topic describe the information that is provided in the details window for each type of design.

Target enrichment design details

· Table: Target enrichment designs - Design details provided for standard custom designs

· Table: Target enrichment designs - Design details provided for catalog and advanced custom designs

Microarray design details

· Table: Microarray designs - Design details provided for standard custom designs

· Table: Microarray designs - Design details provided for catalog and advanced designs

CustomFISH design details

· Table: CustomFISH designs - Design details provided for custom designs

SureGuide design details

· Table: SureGuide designs - Design details provided for custom designs

Also see Actions you can take from the design details window.

Target enrichment design details

Target enrichment designs - Design details provided for standard custom designs

General design information
Design Name	The name of the design.
Design ID	The Agilent-assigned ID number for the design. Each unique design has its own design ID. When you place an order for the design, Agilent uses this number as the design identifier.
Species	The species of the target DNA. The genome build is indicated in parentheses.
Build Version	The genome build for the species.
Category	The type of target enrichment design. The category is only specified for SureSelect DNA, HaloPlex, OneSeq, and ClearSeq designs.
Location	The folder where the design is saved. For designs that you created, you can move the design to a different folder.
Hybridization	The type of hybridization assigned to the design (90 Minute, Overnight, or Not specified). The hybridization type is only used for SureSelect DNA and SureSelect RNA designs.
Design creation information
Status	The status of the design (Draft or Complete). Custom designs have a status of Draft until you finalize the design through the wizard. After finalization, the status changes to Complete. A design must be Complete in order to place an order.
Created By	The name of the user who created the design.
Created On	The date that the design was first created.
Modified On	The date that the design was last edited.
Target information
Target Summary	The target identifiers that were used in probe selection. Each row in this table is a separate target identifier. The table may include the following columns: Target ID - the gene ID, transcript ID, or genomic coordinates that was used to define the target in the design wizard Interval - the bounds of the genomic coordinates where SureDesign mapped the target ID; includes any flanking sequences and UTRs that you selected as regions of interest when creating the design Length or Sequence Length - the total number of base pairs in the target Total Probes - the total number of probes for the target Coverage - the percentage of nucleotides in the target regions of the target ID that are covered by one or more probes in the design # Regions - the number of target regions in the target # Good Coverage - the number of regions within the target ID that have >90% coverage Boosting - the boosting option selected for the probegroup
Target Regions statistics
# Target Regions	The number of target regions in the design.
Size	The size of the genomic footprint of the target regions.
Probes/Sequenced Regions statistics
# Probes / # Amplicons	The total number of probes (SureSelect, OneSeq) or amplicons (HaloPlex, HaloPlexHS) in the design, including replicates.
Size	SureSelect DNA, SureSelect RNA, and OneSeq designs: The total size of the genomic footprint of all the probes in the design, which for SureSelect designs is an approximation of the size of the sequenceable region. HaloPlex and HaloPlexHS designs: The size of the sequenceable region of the design.
Price Tier	The Agilent-assigned pricing category for a design. For HaloPlex and HaloPlexHS designs, Agilent sets the price tier based on the total size of the target regions of interest and the total number of probes in the design. For smaller SureSelect DNA and SureSelect RNA designs, Agilent sets the price tier based on the total capture size of the design. For larger designs, Agilent sets the price tier based on the total number of probes in the design.
Coverage	The coverage of a design is the percentage of nucleotides in the target regions that are expected to be captured by one or more probes/amplicons in the design. For SureSelect DNA, SureSelect RNA, and OneSeq designs, a target nucleotide is considered to be covered if at least one probe comes within 100 bases of the nucleotide in either direction. For HaloPlex and HaloPlexHS designs, a target nucleotide is considered to be covered if the analyzable region of least one amplicon overlaps with the nucleotide. The covered regions are included in the Covered BED file and as a track in the AllTracks BED file. See Design files available for download.

Target enrichment designs - Design details provided for catalog and advanced custom designs

General design information
Design Name	The name of the design.
Design ID	The Agilent-assigned ID number for the design. Each design has a unique design ID. When you place an order for the design, Agilent uses this number as the design identifier.
Species	The species of the target DNA. The genome build is indicated in parentheses.
Location	The file path where the design is saved. For designs that you created, you can move the design to a different folder.
Description	A description of the design. Not all designs have a description. When creating a custom design in an advanced design wizard, you have the option to enter a description, if desired. You can edit the description for designs that you created.
Keywords	The keywords assigned to the design. Not all designs have keywords. When creating a custom design in an advanced design wizard, you have the option to enter keywords, if desired. You can edit the keywords for designs that you create
Hybridization	The type of hybridization assigned to the design (90 Minute, Overnight, or Not specified). The hybridization type is only used for SureSelect DNA and SureSelect RNA designs.
Design creation information
Status	The status of the design (Draft or Complete). Custom designs have a status of Draft until you finalize the design through the wizard. After finalization, the status changes to Complete.
Created By	The name of the user who created the design. Catalog designs are created by Agilent Technologies.
Created On	The date that the design was first created.
Modified On	The date that the design was last edited.
Probegroup/target information
Probegroups Used in the Design	Name and details for the probegroup(s) that comprises the design. Each row in this table is a separate probegroup. The columns in the table are: Name - the name of the probegroup # Probes - the total number of probes in the probegroup, including replicated probes Probe Size - for SureSelect probegroups, probe size is the total size of the genomic footprint of all the probes in the probegroup, which is an approximation of the size of the sequenceable region; for HaloPlex probegroups, probe size is the size of the sequenceable region of the probegroup Replicate Count - the number of times the probegroup is replicated in the design Boosting - the boosting option selected for the probegroup
Probes/Amplicons statistics
# Probes / # Amplicons	The total number of probes (SureSelect DNA, SureSelect RNA, OneSeq) or amplicons (HaloPlex, HaloPlexHS) in the design, including replicates.
Size	SureSelect DNA/RNA and OneSeq designs: The total size of the genomic footprint of all the probes in the design, which for SureSelect designs is an approximation of the size of the sequenceable region. HaloPlex and HaloPlexHS designs: The sum of the target region sizes of the probegroups in the design.

Microarray design details

Microarray designs - Design details provided for standard custom designs

General design information
Design Name	The name of the design.
Design ID	The Agilent-assigned ID number for the design. Each unique design has its own design ID. When you place an order for the design, Agilent uses this number as the design identifier.
Species	The species of the target DNA. The genome build is indicated in parentheses.
Array Format	The number of arrays per slide by the number of features per array.
Control Grid	The Agilent control grid assigned to the design. SureDesign adds a control grid to the design during the probe selection job.
Category	The type of array (CGH or CGH+SNP).
Location	The folder where the design is saved. For designs that you created, you can move the design to a different folder.
Design creation information
Status	The status of the design (Draft or Complete). Custom designs have a status of Draft until you finalize the design through the wizard. After finalization, the status changes to Complete. A design must be Complete in order to place an order.
Created By	The name of the user who created the design.
Created On	The date that the design was first created.
Modified On	The date that the design was last edited.
Target information
Target Summary	The target identifiers that were used in probe selection. Each row in this table is a separate target identifier. The columns in the table are: Target ID - the gene ID, transcript ID, or genomic coordinates that was used to define the target in the design wizard Interval - the bounds of the genomic coordinates where SureDesign mapped the target ID; includes any flanking sequences and UTRs that you selected as regions of interest when creating the design Length - the total number of base pairs in the target regions Coverage - the percentage of nucleotides in the target regions of the target ID that are covered by one or more probes in the design Total Probes - the total number of probes covering that interval Median Probe Spacing - the median number of bp between the starting positions of adjacent probes
Target Regions statistics
# Target Regions	The number of target regions in the design.
Size	The size of the genomic footprint of the target regions.
Probes statistics
# CGH Probes	The number of CGH probes in the design.
CGH Replicates	The number of replicate CGH probes in the design.
Probe Spacing	The number of bp between the starting positions of adjacent probes.
# SNP Probes (CGH+SNP designs only)	The number of SNP probes in the design.
# Norm. Probes	The number of normalization probes in the design.
# Rep. Probes	The number of replicate probes in the design.
# Ctrl. Probes	The number of control probes in the design.
# Backbone Probes	The number of backbone probes in the design.
% Filled	The percentage of features on the slide that have a probe assigned.

Microarray designs - Design details provided for catalog and advanced designs

General design information
Design Name	The name of the design.
Design ID	The Agilent-assigned ID number for the design. Each unique design has its own design ID. When you place an order for the design, Agilent uses this number as the design identifier.
Species	The species of the target DNA. The genome build is indicated in parentheses.
Array Format	The number of arrays per slide by the number of features per array.
Control Grid	The Agilent control grid assigned to the design. SureDesign adds a control grid to the design during the probe selection job.
Category	The type of array (CGH or CGH+SNP).
Location	The folder where the design is saved. For designs that you created, you can move the design to a different folder.
Description	A description of the design. Not all designs have a description. When creating a custom design in an advanced design wizard, you have the option to enter a description, if desired. You can edit the description for designs that you created.
Keywords	The keywords assigned to the design. Not all designs have keywords. When creating a custom design in an advanced design wizard, you have the option to enter keywords, if desired. You can edit the keywords for designs that you created.
Design creation information
Status	The status of the design (Draft or Complete). Custom designs have a status of Draft until you finalize the design through the wizard. After finalization, the status changes to Complete. A design must be Complete in order to place an order.
Created By	The name of the user who created the design.
Created On	The date that the design was first created.
Modified On	The date that the design was last edited.
Probegroup information
Probegroups Used in the Design	Name and details for the probegroup(s) that comprises the design. Each row in this table is a separate probegroup. The columns in the table are: Name - the name of the probegroup # Targets - the number of continuous target regions covered by the probes in the probegroup. Target Size - the total size (in kbp) of all target regions covered by the probes in the probegroup # Probes - the total number of probes in the probegroup, including replicated probes Type - the probegroup type Properties - the properties of the probes in the probegroup (N for normalization probes, R for replicate probes, and F for filler probes) # Reps - the number of replicates of the probegroup included in the design
Probes statistics
# CGH Probes	The number of CGH probes in the design.
# SNP Probes (CGH+SNP designs only)	The number of SNP probes in the design.
# Norm. Probes (CGH and CGH+SNP designs only)	The number of normalization probes in the design.
# Rep. Probes (CGH and CGH+SNP designs only)	The number of replicate probes in the design.
# Ctrl. Probes	The number of control probes in the design.
% Filled	The percentage of features on the slide that have a probe assigned.

CustomFISH design details

CustomFISH designs - Design details provided for custom designs

General design information
Name	The name of the design.
Design ID	The Agilent-assigned ID number for the design. Each completed design has its own design ID. When you place an order for the design, Agilent includes this number as the design identifier. NOTE Break Apart and Dual Fusion designs have two design IDs (one for each design region) which are listed in the Design Summary table.
Category	The category of the design (Single Probe, Break Apart, or Dual Fusion)
Species	The species of the target DNA. The genome build is indicated in parentheses.
Location	The folder where the design is saved. For designs that you created, you can move the design to a different folder.
Design creation information
Status	The status of the design (Draft or Complete). Custom designs have a status of Draft until you finalize the design through the wizard. After finalization, the status changes to Complete. A design must be Complete in order to place an order.
Created By	The name of the user who created the design.
Created On	The date that the design was first created.
Modified On	The date that the design was last edited.
Oligo Summary
Maximum Gap	The size of the largest coverage gap in the design. For Break Apart and Dual Fusion designs, two maximum gap values are listed (one for each design region).
Average GC	The average GC percentage of the oligos in the design. For Break Apart and Dual Fusion designs, two average GC values are listed (one for each design region).
Design Summary
Design Name (Break Apart and Dual Fusion designs only)	The name of the design for the individual design region. Because Break Apart and Dual Fusion designs have two design regions, the oligo set for each design region has its own design name.
Design ID (Break Apart and Dual Fusion designs only)	The Agilent-assigned ID number for each individual design region. Because Break Apart and Dual Fusion designs have two design regions, the oligo set for each design region has its own design ID.
Input Region (Single Probe designs only)	The genomic coordinates of the target region of interest.
Design Region	The genomic coordinates of the design region, including any padding.
Coverage	The percentage of nucleotides in the design region that are covered by one or more oligos in the design.

SureGuide design details

SureGuide designs - Design details provided for custom designs

General design information
Name	The name of the design.
Design ID (Single Probe designs only)	The Agilent-assigned ID number for the design. Each completed design has its own design ID.
Species	The species of the target DNA. The genome build is indicated in parentheses.
Location	The folder where the design is saved. For designs that you created, you can move the design to a different folder.
Design creation information
Status	The status of the design (Draft or Complete). Designs have a status of Draft until you finalize the design through the wizard. After finalization, the status changes to Complete.
Created By	The name of the user who created the design.
Created On	The date that the design was first created.
Modified On	The date that the design was last edited.
Target Details
Target Id	The gene ID, transcript ID, or genomic coordinates that was used to define the target in the design wizard.
Target Co-ordinates	The genomic coordinates where SureDesign mapped the target ID; including any flanking sequences that were selected for inclusion in the design wizard.
Target Window Size	The size of the region within the target that SureDesign uses for gRNA selection.
Input Sequence Size	The size of the target ID, including any flanking sequences that were selected for inclusion in the design wizard.
#gRNA	The number of gRNA sequences that were selected for inclusion in the final design.

Actions you can take from the design details window

· (Advanced HaloPlex designs only) Click BAM to submit a request to generate a simulated BAM file for the design. You will be e-mailed a link to download the file. This action is only available for advanced HaloPlex designs in which the probegroups are a subset of probes from the HaloPlex Exome Agilent Catalog design.

· Click Edit to change the design's description or keywords. This action is only available for advanced designs that you created.

· Click Order to order the design from Agilent or to request a price quote for the design. This action is only available for completed custom designs and catalog designs, and is not applicable to SureGuide designs or to ChIP/CH3 microarray designs.

· Click Delete to delete the design. This action is only available for designs in Draft status.

· Click Download to download one or more files with information on the design.

· Click Move to move the design to a different folder. This action is only available for designs that you created.

· Click UCSC View to launch your internet browser to the UCSC Genome Browser page. The design's AllTracks.bed file is loaded in the browser.

· Click the favorites icon (next to the Design Name) to mark the design as a favorite. The icon turns yellow. Click the favorites icon again to remove a design from your favorites. The icon turns back to gray. Your favorite designs are listed on the SureDesign Home screen, making them quickly accessible.