Sample sheet guidelines for GenomeStudio Genotyping and Methylation

GenomeStudio Genotyping Sample Sheet

A GenomeStudio Genotyping sample sheet is a comma delimited text file (*.csv) that identifies the sample name/ID, beadchip, and array location of each sample in a project. Sample sheet templates are available to download from the various Product Support Files pages for the various beadchip types at Illumina.com. For example, the sample sheet used to create the demo Global Screening Array v3 project can be downloaded here: Infinium Global Screening Array v3.0 Support Files

Following is a screenshot of the demo GSA v3 project samplesheet, viewed in Excel:

Figure 1: Screenshot - GSA-24v3-0_A1_SampleSheet_Demo_12.csv

There are three sections in a sample sheet, "Header", "Manifests", and "Data".

• "Header" is not required, and is user-defined

• "Manifests" contains two columns; the first contains the letter A, the second is populated by the name of the .bpm manifest file to be applied in creating the project, excluding the .bpm extension

• "Data" contains the following columns

Table 1: Genotyping Column headings - Data section

Column	Description	Optional (O) or Required (R)
Sample_ID	Sample identifier (used only for display in the table).	R
SentrixBarcode_A	The barcode of the Array that this sample was hybridized to	R
SentrixPosition_A	The position within the Array this sample was hybridized to	R
Sample_Name	Name of the sample (used only for display in the table).	O
Sample_Plate	The barcode of the sample plate for this sample (used only for display in thetable).	O
Sample_Well	The well within the sample plate for this sample (used only for display in thetable).	O
Gender	Male, Female, or Unknown.	O
Sample_Group	A group, if any, that this sample belongs to (used for exclusion in the Final ReportWizard).	O
Replicates	The Sample_ID of a sample that is a replicate to this sample (used in reproducibility error calculations).	O
Parent1	The Sample_ID of the first parent for this sample.	O
Parent2	The Sample_ID of the second parent for this sample.	O
Path	Directory where your data are stored.	O
Reference	Used for paired sample analysis. Populate this column with the sample ID of the reference sample.	O

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 (See 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 (i.e. “@” 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). Please see the following article for more information regarding correctly formatting barcodes: Important information about using 12-digit BeadChip barcodes in GenomeStudio sample sheets

• 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.

GenomeStudio Methylation Module Sample Sheet

There are some key differences between a Methylation Module sample sheet and a Genotyping Sample Sheet

• The Methylation Module sample sheet does not have a "Manifest" sectioni

• The column headings in the "Data" section have different names

• Certain columns are required to be present, but not to contain information

Table 2: Methylation column headings - Data section

Column	Description	Optional (O) or Required (R)
Sample_Name	Name of the sample	O
Sentrix_ID	The barcode of the Array that this sample was hybridized to	R
Sentrix_Position	The position within the Array this sample was hybridized to	R
Sample_Plate	The barcode of the sample plate for this sample (used only for display in the table)	O
Sample_Group	User-specified name of the sample group - The column must be present, but data entry is optional	R
Pool_ID	Legacy column -Column must be present on sample sheet, but should not contain any information	R

Figure 2: Screenshot - MethylationEPIC sample sheet

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