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TCGA sample names for .idat files

How can I map sample names (TCGA-XX-XXXX*) to .idat filenames for TCGA data? There must be a key somewhere, but I cannot seem to be able to find it.

For example, the .idat files are here: https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/laml/cgcc/jhu-usc.edu/humanmethylation450/methylation/jhu-usc.edu_LAML.HumanMethylation450.Level_1.2.5.0/

The corresponding processed files have sample names: https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/laml/cgcc/jhu-usc.edu/humanmethylation450/methylation/jhu-usc.edu_LAML.HumanMethylation450.Level_3.2.5.0/

tcga tcga
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updated by jananiharan • jananiharan • written by igor igor

1 answer

When you download TCGA data, you should get a file named file_manifest.txt. This contains the sample barcode and the corresponding .idat file name.

For eg.:

Disease Platform Type Center Platform Level Barcode File Name BRCA DNA Methylation JHU_USC HumanMethylation450 Level_1 TCGA-BH-A1FE-11B-14D-A13T-05 6026818132_R02C01_Grn.idat BRCA DNA Methylation JHU_USC HumanMethylation450 Level_1 TCGA-E9-A1NA-11A-33D-A145-05 6026818122_R05C02_Red.idat

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written by jananiharan • jananiharan

Yes, I realize there exists a file like that. Where do I find it?

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written by igor igor

It should be automatically generated when you download TCGA data. When you unzip the tarball, you should see this file.

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written by jananiharan • jananiharan

I provided links specifically to illustrate that is not the case.

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written by igor igor

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