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Table 3 Method performance on targeted 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) 0.58
Star.htseq.ine STAR, HTSeq (intersection-nonempty) 0.76
Star.htseq. is STAR, HTSeq (intersection-strict) 0.75
Tophat.htseq. u TopHat2, HTSeq (union) 0.58
Tophat.htseq.ine TopHat2, HTSeq (intersection-nonempty) 0.75
Tophat.htseq. is TopHat2, HTSeq (intersection-strict) 0.75
Star.cufflinks STAR, Cufflinks 0.90
Star.cufflinks.mr STAR, Cufflinks (multi-read-correct) 0.83
Tophat.cufflinks TopHat2, Cufflinks 0.90
Tophat.cufflinks.mr TopHat2, Cufflinks (multi-read-correct) 0.82
Sailfish Sailfish (RPKM) 0.85
Sailfish Sailfish bias-corrected (RPKM) −0.14
  1. Pearson correlation coefficients between FPKM from each method and the expected FPKM from simulated data for 958 difficult genes