What are the best tools for quantifying allele-specific expression from bulk RNA-seq data these days?

Question

[Paulo]

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!

[LauferVA]

• Do you have DNA sequencing on same samples or should I assume you just have bulk RNA seq only
• Can you clarify if this is germline or somatic?
• How many samples do you have?

[Paulo]

• I also have whole-genome data, which I’ve already processed for variant calling using GATK tools.
• This is germline and I have 15 samples.