I’ve been using phASER (https://github.com/secastel/phaser) for allele-specific expression (ASE) analysis from bulk RNA-seq experiments, and I’ve found it to be quite easy and straightforward to use. However, I’ve realized that phASER doesn't account for strand-specific information, which is problematic for my data. Specifically, I end up getting the same haplotype/SNP counts for overlapping genes, which doesn’t seem ideal.

Are there any tools available that handle ASE quantification while also considering strand-specificity? Ideally, I’m looking for something that can accurately account for overlapping genes and provide reliable results. Any recommendations or insights into tools like ASEReadCounter, HaploSeq, SPLINTER, or others would be greatly appreciated!