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Table 3 Fraction of genes where the expression count bias is less than a factor of two

From: Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching

Alignment and count method Hom. coverage Inhom. coverage Mod. TSS + polyA
STAR-countOverlaps 0.892 0.892 0.892
tophat-countOverlaps 0.893 0.893 0.893
STAR-htseq 0.877 0.877 0.877
tophat-htseq 0.883 0.883 0.883
RSEM-count 0.929 0.929 0.929
RSEM-posteriorCount 0.930 0.930 0.930
  1. For each gene we estimate expression in terms of read count and report the fraction of genes for which the estimate is less than a factor of two different from the number of correctly aligned reads. We consider the alignments produced by STAR and tophat in combination with subsequent counting of the overlapping reads using HTSeq and the countOverlaps method. The RSEM software performs alignment and expression counting. Here we list the results for the reported counts as well as the results for the posterior estimates of the counts.