Table 1 Method description
From: Errors in RNA-Seq quantification affect genes of relevance to human disease
Method | Aligner | Quantification | Quantification notes |
|---|---|---|---|
star.htseq. u | STAR 2.4.0 | htseq-count (HTSeq 0.6.1) | -m union |
star.htseq.ine | STAR 2.4.0 | htseq-count (HTSeq 0.6.1) | -m intersection-strict |
star.htseq. is | STAR 2.4.0 | htseq-count (HTSeq 0.6.1) | -m intersection-nonempty |
tophat.htseq. u | TopHat 2.0.12 | htseq-count (HTSeq 0.6.1) | -m union |
tophat.htseq.ine | TopHat 2.0.12 | htseq-count (HTSeq 0.6.1) | -m intersection-strict |
tophat.htseq. is | TopHat 2.0.12 | htseq-count (HTSeq 0.6.1) | -m intersection-nonempty |
star.cufflinks | STAR 2.4.0 | Cufflinks 2.2.1 | Â |
star.cufflinks.mr | STAR 2.4.0 | Cufflinks 2.2.1 | --multi-read-correct |
tophat.cufflinks | TopHat 2.0.12 | Cufflinks 2.2.1 | Â |
tophat.cufflinks.mr | TopHat 2.0.12 | Cufflinks 2.2.1 | --multi-read-correct |
sailfish | NA | Sailfish 0.6.3 | quant.sf |
sailfish | NA | Sailfish 0.6.3 | quant_bias_corrected.sf |