Sample sheet guidelines for GenomeStudio

The sample sheet is a comma separated value (\*.csv) file that identifies the name, chip, and array location of each sample in a project. Sample sheet templates are available to download from the Product Support Files page at Illumina.com (Demo Sample Sheet). In order to avoid errors during the project creation step, follow the guidelines below for creating a sample sheet.

• The format of the sample must match the template, including the complete header section, the data section, and all column names.

• Fill in the required columns: Sample ID, Sentrix_ID, and Sentrix_Position. Other columns are optional (Table 1).

• The Sentrix ID and Sentrix Position must match the intensity data (.idat) files that will be loaded to create the project.

• Only list samples that have the .idat files in the parent folder. Do not list any other samples.

• File names must only contain alphanumeric characters, underscores, and dashes. Introducing invalid characters, such as spaces, or symbols, such as “@” or “#,” will result in errors.

• The manifest name in the sample sheet must match the exact filename of the .bpm file that will be used for the analysis.

• If using Excel, make sure barcodes are not displayed in scientific notation. Excel will automatically convert the BeadChip barcodes to scientific notation and will not save to the .csv file correctly. The BeadChip barcodes must be formatted correctly before saving (every time the file is saved).

• Save the sample sheet as a comma separated value text file (\*.csv).

• Check the final sample sheet for accuracy by opening it with Notepad.

  • Make sure that the delimiter is a comma. GenomeStudio is unable to parse a sample sheet if semi-colons, tabs, or other delimiters are present in the file.

  • Check for extra lines with blank information. These lines are identified by GenomeStudio as additional samples and are not visible when viewed in Excel (but can be seen in a standard text editor like Notepad).

  • Remove the extra lines from the sample sheet by selecting and deleting them in Notepad.

• If the sample sheet is not recognized, rename the sample sheet with a simple name, such as Sample_Sheet.csv.

Data Section The first row of the Data section must indicate the column names of the data to follow. The columns can be in arbitrary order, and additional user-defined columns can be included in the file.

Example of a Genotyping Array Sample Sheet

Example of a MethylationEPIC Array Sample Sheet

For any feedback or questions regarding this article (Illumina Knowledge Article #3223), contact Illumina Technical Support [e-mail].