Skip to main content

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  
star.cufflinks.mr STAR 2.4.0 Cufflinks 2.2.1 --multi-read-correct
tophat.cufflinks TopHat 2.0.12 Cufflinks 2.2.1  
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
  1. A description of the RNA-Seq alignment and quantification methods used. NA not applicable