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 |