Does anyone have experience with standard rna-seq analysis tools (edgeR, DESeq2, etc) to detect allele-specific expression? I have a count table in which each F1 hybrid (3 biological replicates) has separate counts for the paternal and maternal allele. I am considering implementing a paired design in edgeR to test for differential allele expression between the parental alleles. However, I have not seen any publications using edgeR or DESeq2 to analyze ASE, so I would like to know if there is an underlying reason why these tools would be inappropriate for this type of analysis.
Though there are some rna-seq analysis tools specifically designed for ASE, most assume a binomial distribution, which is not appropriate for count data.