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Table 1 A comparison of ASE call rates for original mapped data and after normalization, for four different alignment methods

From: A haplotype-based normalization technique for the analysis and detection of allele specific expression

Method True Positives False Positives True Negatives False Negatives Sensitivity Specificity Precision
Tophat2 108.2 452.4 11281.0 74.6 59.15 % 96.14 % 19.32 %
Tophat2 Normalized 110.4 94.0 11639.4 72.4 60.33 % 99.20 % 53.90 %
STAR 130.8 87.6 11666.8 52.4 71.40 % 99.25 % 58.87 %
STAR Normalized 135.2 40.2 11714.2 48.0 73.75 % 99.66 % 77.03 %
TH2_5MM 149.6 50.6 11702.8 33.4 81.78 % 99.57 % 74.72 %
TH2_5MM Normalized 148.2 20.0 11733.4 34.8 80.97 % 99.83 % 88.03 %
STAR (No clip) 151.6 51.4 11703.0 31.6 82.66 % 99.56 % 74.61 %
STAR (No clip) Normalized 152.0 30.0 11724.4 31.2 82.91 % 99.74 % 83.50 %
  1. In all cases, the true number of significant ASE events averaged across five simulations is 183.2