This repository contains code to implement the model of allele-specific expression (ASE) described in Skelly et al. 2011 Genome Research doi:10.1101/gr.119784.110.

The directory biased_SNPs provides code to implement the model for detecting biased SNPs from DNA data. These SNPs are then filtered out for all subsequent analyses. This model is described in section S1.3.1 of the supplementary material. See the README in that directory for more details.

The directory DNA_model provides code to implement the model for genomic DNA read counts that estimates overdispersion in this "null" data where no genes should show ASE. This model is described in section 1.3.2 of the supplementary material. See the README in that directory for more details.

The directory RNA_model provides code to implement the model to detect ASE in read counts derived from RNA. This model is described in section 1.3.3 of the supplementary material. See the README in that directory for more details.

This tutorial (PDF) provides an overview of how to use scripts in the DNA_model/orig and RNA_model/orig directories to implement our statistical model for ASE. These are the scripts that were originally released with the paper and are available on the Genome Research website as supplementary information. They have a few corrections from the exact code published on the Genome Research website to account for bugs discovered after publication as well as changes to dependencies that the code utilizes.