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The functionality described in this
topic is only available when you mark Show
Advanced Options.
Define Probegroup
In this step, complete the fields described below to define the probegroup.
Design Category
Select the type of HaloPlex design that you want to create.
· HaloPlex - Select HaloPlex to create a HaloPlex probegroup that does not include molecular barcodes. If you are using the Ion Torrent PGM, you must select this option.
· HaloPlexHS - Select HaloPlexHS to create a HaloPlex probegroup that includes molecular barcodes in the adaptor sequences. During analysis of the sequencing data, molecular barcodes enable molecule tracking for removal of PCR duplicate reads.
Probegroup Name
Type a name for your design into the field. Alphanumeric characters, hyphens, underscores, and spaces are permitted. The name must be unique within your workgroup.
Species
For HaloPlex designs, the species is set to H. sapiens.
Build
Select the desired genome build in the provided drop-down list.
If no drop-down list for build selection is provided, that indicates that only one genome build is currently available. That build is indicated below the Species field.
Create In
Specify the folder in which you want to save this design. The default selection is the top-level folder for your workgroup.
To change the selection, click Select to open the Select Folder dialog box, and mark the folder in which you want to save the new design. This dialog box lists the available folders within your workgroup and, if you are a member of any collaborations, lists the collaboration folders to which you have access. (If you later decide you want to change the folder location of the design, you can move it to another folder.)
Platform
Select a sequencing platform from the drop-down list. HaloPlex designs are platform-specific. If you will be sequencing on multiple platforms, you need to create a separate HaloPlex design for each platform.
Read Length
If you selected Illumina as the platform, select a read length (in base pairs) for your sequencing reactions in the Read Length drop-down list.
The read length is used to determine if the analyzable region of an amplicon will contribute to coverage of a target region. The HaloPlex algorithm iteratively adds longer and shorter amplicons to maximize coverage. Changing the read length from 100 bp to 150 bp may slightly alter the results of probe selection.
When you select a read length of 250 bp, SureDesign uses the same probe selection algorithm as it uses for 100-bp and 150-bp read lengths, but it uses a different coverage calculation to account for the longer coverage contribution per amplicon.
If you intend to use the design for multiple read lengths (e.g. HiSeq at 100 bp and MiSeq at 150 bp), Agilent recommends that you select the longer read length in this drop-down.
Description
(Optional) Type a description of the design. The description can be up to 2000 characters. Use only alphanumeric characters (a-z, A-Z, and 0-9) and the following special characters: _, -, $, #, @.
Keywords
(Optional) Type one or more keywords for the design, separated with a comma or space. You can type up to 2000 characters in this field. Use only alphanumeric characters (a-z, A-Z, and 0-9), commas, dashes, and underscores in your keywords. You can later use these keywords to search for the design.
Click Next to advance to the Add
Content step.