├── .gitignore ├── DNA_model ├── DNAmodel.R ├── DNAmodel_exctract_results.R └── readGzippedMcmcOutput.R ├── README.md ├── RNA_model ├── RNAmodel.R ├── RNAmodel_exctract_results.R ├── merge_ASE_with_Gene.sh └── readGzippedMcmcOutput.R ├── find_biased_SNPs ├── biased_snps.bug ├── biased_snps_rjags.R ├── extract_unbiasedRNA.sh ├── find_unbiasedDNA.R └── merge_by_Genes.sh ├── hybrid-genome-reference-mapping ├── calls.py └── hybrid_reference_maker.py ├── make_ASEReadCounter_InputVCF.py ├── phaseASEReadCounter_GeneSplit.py └── skelly_original ├── DNA_model ├── README.md └── orig │ ├── DNAmodel.R │ └── readGzippedMcmcOutput.R ├── GenomeBiology.bst ├── LICENSE.md ├── Makefile ├── README.md ├── RNA_model ├── README.md └── orig │ ├── RNAmodel.R │ └── readGzippedMcmcOutput.R ├── biased_SNPs ├── .directory ├── .gitignore ├── README.md ├── calculate_posterior_prob_biased.R ├── orig │ ├── 2componentNullModel.bySNP.R │ ├── generic_MCMC.R │ └── run_test.R ├── rjags │ ├── biased_snps.bug │ ├── 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