{"id":4806,"date":"2022-05-11T23:34:36","date_gmt":"2022-05-12T03:34:36","guid":{"rendered":"https:\/\/labs.icahn.mssm.edu\/minervalab\/?p=4806"},"modified":"2022-05-11T23:34:39","modified_gmt":"2022-05-12T03:34:39","slug":"tcga","status":"publish","type":"post","link":"https:\/\/labs.icahn.mssm.edu\/minervalab\/tcga\/","title":{"rendered":"tcga"},"content":{"rendered":"

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Scientific Computing and Data<\/a> \/ Research Data Services<\/a> \/\u00a0Data Ark: Data Commons<\/a> \/ TCGA<\/p>\n

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TCGA – The Cancer Genome Atlas Program<\/span><\/strong><\/h1>\n

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The Cancer Genome Atlas(TCGA)<\/a> is a landmark cancer genomics program, that molecularly characterized over 20,000 primary cancer and matched normal samples spanning 33 cancer types. The program is a joint effort between National Cancer Institute and the National Human Genome Research Institute since 2016.\u00a0<\/span><\/p>\n

Currently, two versions are hosted on the Data Ark. Version 31.0 and version 32.0. The gene model used as a reference across TCGA has been updated from GENCODE 22(GRC37\/hg19)—version 31 to GENCODE 36 (GRCh38\/hg38)–version32. To learn more about the data sets from a different version, find the data release notes <\/span>here<\/span><\/a><\/p>\n

All the TCGA data sets downloaded belong to the \u201copen-access\u201d category and were obtained from the Genomic Data Commons Data Portal.<\/a><\/span><\/p>\n

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TCGA Processed Data Sets<\/h2>\n\n\n\n\n\n\n\n\n\n\n\n
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TCGA Processed data sets<\/h1>\n

The TCGA RNA-seq counts files have been processed into 33 folders.<\/p>\n

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To use this data, NO\u00a0DUA form<\/strong> is required, you can access the data at the following path on Minerva – <\/span>\/sc\/arion\/projects\/data-ark\/Public_Unrestricted\/gnomAD\u00a0<\/span><\/span> or you can load module $ module load dataark <\/strong>to see the path variables.\u00a0<\/span><\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n

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Data Ark Data Sets<\/h1>\n

Public data sets (unrestricted)<\/strong><\/p>\n