QuickBEAST is a robust and scalable Bayesian model for estimating allele-specific expression (ASE) from high-throughput sequencing data. It is used in BEASTIE, designed for fast application across large numbers of simulations. It estimates the binomial proportion p representing Allele-Specific Expression (ASE). The primary output, qb_mode, is the Maximum A Posteriori (MAP) effect size (mode of p) estimated via a subgrid search algorithm. Additionally, empirical p values are computed from 1000 null simulations for each gene. The ASE effect size (θ) is then calculated downstream using the relation (θ = p/(1-p)), providing a precise quantification of the expression bias between alleles.
apt-get install libgsl-dev
make
- Format: The data is presented in a tab-delimited text file without headers.
- Fields:
- geneID: Identifier for the gene.
- #hetX: X denotes the number of heterozygous sites.
- ALTn_allele_count and REFn_allele_count: Allele counts at the nth heterozygous site.
- pi(n-1): n−1 π values, where each π is a switching error parameter for each SNP pair.
geneID 1 ALT1_allele_count REF1_allele_count
geneID 2 ALT1_allele_count REF1_allele_count ALT2_allele_count REF2_allele_count pi
geneID 3 ALT1_allele_count REF1_allele_count ALT2_allele_count REF3_allele_count ALT3_allele_count REF2_allele_count pi1 pi2
in_file = test_data/bimodal_genes
out_qb_file = bimodal_genes_qb
./QuickBEAST --alpha 8.789625 --beta 8.789625 --mean --mode -f $in_file --fixMaxHetSite > $out_qb_file
Please cite this paper when using QuickBEAST for your publications.
Zou, X., Gomez, Z. W., Reddy, T. E., Allen, A. S., Majoros, W. H. (2024). Bayesian Estimation of Allele-Specific
Expression in the Presence of Phasing Uncertainty. bioRxiv, doi: 10.1101/2024.08.09.607371.
- Special thanks to William H. Majoros for his guidance and support.
- Thanks to the Allen Lab for providing the resources and environment to develop QuickBEAST.
If you have any questions, feel free to reach out to me at Xue Zou.