RNA-Seq Quantification

RNA-Seq quantification is used to generate gene expression levels from mRNA and miRNA sequence data.

Gene Expression Quantification Pipeline

For mRNA-Seq data, the GDC generates gene level and exon level quantification in Fragments Per Kilobase of transcript per Million mapped reads (FPKM). To facilitate cross-sample comparison and differential expression analysis, the GDC also provides Upper Quartile normalized FPKM (UQ-FPKM) values and raw mapping count.

In addition, the GDC generates miRNA profiling with a pipeline developed by the University of British Columbia [1]. This pipeline removes adaptor sequences from raw reads, aligns these short reads, and then assigns aligned reads to miRNA features from miRBase for quantification.

[1]. Chu A, Robertson G, Brooks D, Mungall AJ, Birol I, Coope R, Ma Y, Jones S, Marra MA. Nucleic Acids Res. 2015 Aug 13. pii: gkv808. Large-scale profiling of microRNAs for The Cancer Genome Atlas.