ASEQ pipeline and detection power of SNP-based ASE studies. A) Illustration of ASEQ pipeline used to perform ASE analysis. Given an initial list of SNPs (or genomic coordinates) and DNA-seq data, the GENOTYPE mode determines for each sample the set of heterozygous SNPs. Then, the heterozygous SNPs are analyzed with the ASE mode in the context of the corresponding matched RNA-seq samples data and a list of genes (only coding SNPs will contribute to the analysis). A final collection of sample-based and aggregated ASE results is generated. (The GENOTYPE mode works for any set of genomic positions independently from SNP annotations). B) Frequency distribution of coding SNPs per gene. Frequency distribution of genes containing N = 1,2,… coding SNPs based on UCSC hg19 gene catalogue and dbsnp 138 CEU. Note that the number of genes containing at most 14 SNPs corresponds to the 99 percentile of the distribution. C) Upper-limit of genes available for ASE calculation for different heterozygous SNPs frequencies. Upper-limit computation trends of the number of genes available for ASE calculation considering different heterozygous sites frequencies. Few SNPs per genes are enough to rapidly converge to the T
estimate. D) HapMap frequency distribution of heterozygous SNPs frequencies. Distribution of heterozygous SNPs frequency obtained from CEU HapMap samples. E) Distribution of genes available for ASE calculation. Empirical distribution of ASE suitable genes is shown; horizontal line corresponds to the T
for SNPs frequency equal to 30%.