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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
For any feedback or questions regarding this article (Illumina Knowledge Article #8510), contact Illumina Technical Support [email protected].
Last modified 25d ago
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