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

BMC Bioinformatics

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

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 %

In all cases, the true number of significant ASE events averaged across five simulations is 183.2

ISSN: 1471-2105