How to format file path for DRAGEN Array IDAT sample sheet and GTC sample sheet for Windows OS

IDAT Sample Sheet

Local Analysis: IDAT sample sheet can be a CSV or JSON formatted file with direct paths to sample IDAT files to enable analysis of samples from different directories.

CSV format for Linux:

Green IDAT Path,Red IDAT Path/path/to/sample1_Grn.idat,/path/to/sample1_Red.idat/path/to/sample2_Grn.idat,/path/to/sample2_Red.idat/path/to/sample3_Grn.idat,/path/to/sample3_Red.idat  

CSV format for Windows (use double backslash):

Green IDAT Path,Red IDAT Path\\path\\to\\sample1_Grn.idat,\\path\\to\\sample1_Red.idat\\path\\to\\sample2_Grn.idat,\\path\\to\\sample2_Red.idat\\path\\to\\sample3_Grn.idat,\\path\\to\\sample3_Red.idat  

JSON format for Linux:

[{"Green IDAT Path": "/path/to/sample1_Grn.idat","Red IDAT Path": "/path/to/sample1_Red.idat"},{"Green IDAT Path: "/path/to/sample2_Grn.idat","Red IDAT Path": "/path/to/sample2_Red.idat"},{"Green IDAT Path": "/path/to/sample3_Grn.idat","Red IDAT Path": "/path/to/sample3_Red.idat"},]  

JSON format for Windows (use double backslash):

[{"Green IDAT Path": "\\path\\to\\sample1_Grn.idat","Red IDAT Path": "\\path\\to\\sample1_Red.idat"},{"Green IDAT Path: "\\path\\to\\sample2_Grn.idat","Red IDAT Path": "\\path\\to\\sample2_Red.idat"},{"Green IDAT Path": "\\path\\to\\sample3_Grn.idat","Red IDAT Path": "\\path\\to\\sample3_Red.idat"},]  

Cloud analysis: The IDAT sample sheet can be a CSV formatted file.

beadChipName,sampleSectionName204753010023,R01C01204753010023,R02C01204753010024,R01C01204753010024,R02C01  

GTC Sample Sheet

Local Analysis: GTC sample sheet can be a CSV or JSON formatted file with direct paths to sample GTC files to enable analysis of samples from different directories.

CSV format for Linux:

GTC Path/path/to/sample1.gtc/path/to/sample2.gtc/path/to/sample3.gtc  

CSV format for Windows (use double backslash):

GTC Path\\path\\to\\sample1.gtc\\path\\to\\sample2.gtc\\path\\to\\sample3.gtc  

JSON format for Linux:

[{"GTC Path": "/path/to/sample1.gtc"},{"GTC Path": "/path/to/sample2.gtc"},{"GTC Path": "/path/to/sample3.gtc"}]  

JSON format for Windows (use double backslash):

[{"GTC Path": "\\path\\to\\sample1.gtc"},{"GTC Path": "\\path\\to\\sample2.gtc"},{"GTC Path": "\\path\\to\\sample3.gtc"}]  

For more information, refer to the following:* DRAGEN Array User Guide

• DRAGEN Array Secondary Analysis Software Downloads under section 'DRAGEN Array Sample Sheet Templates'

For any feedback or questions regarding this article (Illumina Knowledge Article #8510), contact Illumina Technical Support [email protected].