# 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). | --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. 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