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

BMC Bioinformatics

Table 2 A comparison of ASE call rates for three different approaches: a filtering methods, mapping to two parental genomes and our normalization approach

Mapping procedure	Control Method	True Positives	False Positives	True Negatives	False Negatives	Sensitivity	Specificity	Precision
TH2_5MM	Normalized	142.28	19.80	11737.80	36.80	79.42 %	99.83 %	87.69 %
TH2_5MM	Two Genomes	144.96	21.84	11737.68	34.44	80.84 %	99.81 %	86.85 %
TH2_5MM	Filtered	117.44	46.12	11711.48	61.64	65.71 %	99.61 %	71.77 %
STAR (No clip)	Normalized	147.40	29.00	11729.24	31.80	82.28 %	99.75 %	83.52 %
STAR (No clip)	Two Genomes	152.24	22.28	11724.96	27.16	84.80 %	99.81 %	87.17 %
STAR (No clip)	Filtered	122.68	43.72	11714.52	56.52	68.53 %	99.63 %	73.70 %

ISSN: 1471-2105