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Table 2 Method performance on global simulated data

From: Errors in RNA-Seq quantification affect genes of relevance to human disease

Method Description Pearson correlation coefficient
Star.htseq. u STAR, HTSeq (union) 0.78
Star.htseq.ine STAR, HTSeq (intersection-nonempty) 0.88
Star.htseq. is STAR, HTSeq (intersection-strict) 0.86
Tophat.htseq. u TopHat2, HTSeq (union) 0.78
Tophat.htseq.ine TopHat2, HTSeq (intersection-nonempty) 0.87
Tophat.htseq. is TopHat2, HTSeq (intersection-strict) 0.86
Star.cufflinks STAR, Cufflinks 0.95 STAR, Cufflinks (multi-read-correct) 0.91
Tophat.cufflinks TopHat2, Cufflinks 0.95 TopHat2, Cufflinks (multi-read-correct) 0.90
Sailfish Sailfish (RPKM) 0.95
Sailfish Sailfish bias-corrected (RPKM) 0.08
  1. Pearson correlation coefficients between FPKM from each method and the expected FPKM from simulated data for 19,654 human protein-coding genes. RPKM reads per kilobase per million (see “Materials and Methods”)