Input Target Files

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:

Genotyping

• Gene (Human only)

• Region (Human only)

• Identity (Human only)

• Sequence

• Existing design

• Score

Methylation

• Gene (Human only)

• Region

• Identity

• Co-ordinates

Refer to the following sections for information on the contents of the input target files:

Gene (Genotyping/Human Only)

Field	Description
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.

Region (Genotyping/Human Only)

Field	Description
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.

Identity (Genotyping/Human Only)

Field	Description
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.

Sequence (Genotyping)

Column	Description
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.

Existing Design (Genotyping)

Field	Description
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.

Score (Genotyping)

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 (Methylation/Human Only)

Field	Description
Gene_Name	Gene name.

Region (Methylation)

Field	Description
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.

Identity (Methylation)

Field	Description
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.

Coordinate (Methylation)

Field	Description
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).