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Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results

24 Jul 2015

Abstract excerpt

MOTIVATION: The Cancer Genome Atlas (TCGA) RNA-Sequencing data are used widely for research. TCGA provides 'Level 3' data, which have been processed using a pipeline specific to that resource. However, we have found using experimentally derived data that this pipeline produces gene-expression values that vary considerably across biological replicates. In addition, some RNA-Sequencing analysis tools require...

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PMID: 26209429
DOI: 10.1093/bioinformatics/btv377

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