Input target files contain information for the requested targets. To download templates of input target file formats, select Download File Templates from the Upload Targets screen. Use a text editor or spreadsheet program to enter custom targets into the template file (*.csv).
The types of files that can be uploaded as input target files include:
Gene (Human only)
Region (Human only)
Identity (Human only)
Sequence
Existing design
Score
Gene (Human only)
Region
Identity
Co-ordinates
Refer to the following sections for information on the contents of the input target files:
Gene_Name
Gene name.
Bases_Upstream
Search database for targets with coordinates greater than the gene start position. For example, entering 1000 bases upstream to include and search dbSNP for any rsIDs within 1000 base pairs above the gene coordinates.
Bases_Downstream
Search database for targets with coordinates less than the gene start position. For example, entering 1000 bases downstream to include and search dbSNP for any rsIDs within 1000 base pairs below the gene coordinates.
Chromosome
Chromosome name.
Start_Coordinate
Search databases for targets with coordinates greater than start coordinate.
End_Coordinate
Search database for targets with coordinate less than end coordinate.
Locus Name
Locus name. Enter rsID for the locus. Valid characters: alphanumeric, numbers, hyphens, and underscores. Example: rs1234567.
Replication_Count
Replicate the design targets in output files. Select no repeat (1), duplicate (2), or triplicate (3). Valid characters: 1, 2, 3.
Locus_Name
Locus name. Valid characters: alphanumeric, numbers, hyphens, and underscores.
Target_Type
Target type. Enter SNP or INDEL.
Sequence
Loci sequence. Specified sequence must have greater than 50 base pairs on both sides of the variant.
Chromosome
Locus chromosome name.
Coordinate
Genomic position start.
Genome_Build_Version
Genome build version. Example: 38.
Source
Reported source of the sequence and annotation data. Example: dbSNP.
Source_Version
Source version number.
Sequence_Orientation
Direction that was selected for primer DNA synthesis. Can be forward, reverse or unknown. Selecting unknown makes it impossible to run a strand report later.
Plus_Minus
DNA strand orientation.
Species
Species name. Example: human.
Force_Infinium_I
Force the design using Infinium I chemistry. Enter TRUE to force Infinium II SNPs to be designed as Infinium I. Enter FALSE for content to be designed as recommended.
Replication_Count
Replicate the design targets in output files. Select no repeat (1), duplicate (2), or triplicate (3). Valid characters include: 1, 2, 3.
Ilmn_ID
Illumina ID from existing designs.
Species
Species name. Example: human.
Force_Infinium_I
Force the design using Infinium I chemistry. Enter TRUE to force Infinium II SNPs to be designed as Infinium I. Enter FALSE for content to be designed as recommended.
The score file is produced as an output file by DesignStudio and contains targets from the score file data section of the existing design that produced it. The output score file can be used as input after the headers have been removed.
Gene_Name
Gene name.
Chromosome
Chromosome name.
Start_Coordinate
Search databases for targets with coordinates greater than start coordinate.
End_Coordinate
Search database for targets with coordinate less than end coordinate.
Locus_name
Locus name. Valid characters: alphanumeric, numbers, hyphens, and underscores.
MostImportant
When the mostImportant parameter is set to TRUE, the system will replicate the target three times.
Chromosome
Chromosome name.
Locus_Name
Locus name. Valid characters: alphanumeric, numbers, hyphens, and underscores.
Position_Start
Value of coordinate that is location of the target.
Type
Type of the target(CpG/CpH).
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