# Target Files Common Errors

***

**Genotyping Common Errors**

| Target Files    | Input Format/Source                                                                                                                                                                                                                                                                                              | Common Errors                                                                                                                                                                                                    |
| --------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Identity List   | <ul><li>rsID numbers from dbSNP.</li><li>Known markers described in the dbSNP.</li></ul>                                                                                                                                                                                                                         | Duplicate rsID numbers, RNA, or nonbiallelic SNPs. The sequence associated with the rsID may change over time based on the dbSNP Build. View the DesignStudio homepage for the dbSNP build currently referenced. |
| Sequence List   | <p>Sequence includes:</p><ul><li>SNPs: (...AGC\[G/T]AC...).</li><li>Indels: (...TGC\[-/AG]CCG...).</li></ul><p>The file template must have an additional species column for XT iSelect.</p><ul><li>Markers from private databases.</li><li>Requires a minimum of 50 bp sequence on either side of SNP.</li></ul> | <ul><li>Locus names that begin with rs or cg, or contain characters (%/='?@;\`,\_ or space).</li><li>Duplicate probe names.</li><li>SNP/Indel not annotated properly.</li></ul>                                  |
| Region List     | <ul><li>Chromosome, start and end coordinate.</li><li>List of chromosomal regions that are referenced from dbSNP.</li></ul>                                                                                                                                                                                      | <ul><li>Repetitive regions.</li><li>Markers with ambiguous or multiple loci.</li></ul>                                                                                                                           |
| Gene List       | <ul><li>Gene Name RefSeq accession ID or HUGO ID.</li><li>Bases upstream and downstream.</li><li>Provides design of all markers with a gene along upstream and downstream regions.</li></ul>                                                                                                                     | File includes 600 genes or more or upstream and downstream regions are 10,000 or more bases, which exceeds the 1 million SNPs limit per file.                                                                    |
| Existing Design | <ul><li>List of ILMN IDs from previous designs for iSelect, XT iSelect, or Illumina commercial assays.</li><li>Requires an additional species column for XT iSelect ILMN ID.</li></ul>                                                                                                                           | <ul><li>Duplicate probe names.</li><li>Species don't match between Illumina original design and input file.</li></ul>                                                                                            |
| SNP Score File  | <ul><li>Microarray Designer generates the score file.</li><li>Before importing, remove the header section above the Locus\_Name.</li><li>Requires an additional species column for XT iSelect.</li></ul>                                                                                                         | Header section above locus name is not removed.                                                                                                                                                                  |

**Methylation Common Errors**

| Target Files | Input Format/Source                                                            | Common Errors                                                                                                                                                                                                                                                                                                                                                                   |
| ------------ | ------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Identity     | <ul><li>Locus\_name</li><li>MostImportant</li></ul>                            | <ul><li>Locus\_Name must not be empty.</li><li>MostImportant must not be empty.</li><li>MostImportant must be a valid boolean.<br></li></ul>                                                                                                                                                                                                                                    |
| Coordinates  | <ul><li>Locus\_name</li><li>Chromosome</li><li>Position\_start</li></ul>       | <ul><li>Chromosome must not be empty.</li><li>Position\_Start must not be empty.</li><li>Position\_Start must be a valid number.</li><li>Type (VariantType) must not be empty.</li><li>Type (VariantType) must be of value 'cg' or 'ch'.</li></ul>                                                                                                                              |
| Gene         | <ul><li>Gene\_Name</li></ul>                                                   | <ul><li>Gene\_Name must not be empty.</li></ul>                                                                                                                                                                                                                                                                                                                                 |
| Region       | <ul><li>Start\_Coordinate</li><li>End\_Coordinate</li><li>Chromosome</li></ul> | <ul><li>Chromosome must not be empty.</li><li>End\_Coordinate must not be empty.</li><li>Start\_Coordinate must be a valid number.</li><li>End\_Coordinate must be a valid number.</li><li>Start\_Coordinate must be less than or equal to End\_Coordinate.</li><li>Start\_Coordinate cannot be a negative number</li><li>End\_Coordinate cannot be a negative number</li></ul> |

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