Inquiry regarding UMI deduplication and PCR bias mitigation for ASE analysis

[Arsenalwins]

Thank you for developing this powerful tool！

I have a question regarding the handling of PCR bias. As scRNA-seq (e.g., 10x Genomics) often involves extensive PCR amplification, I am concerned whether Monopogen explicitly accounts for UMI (Unique Molecular Identifier) tags during the variant calling or the generation of the counts.mtx (ref/alt counts).Specifically:Does Monopogen perform UMI deduplication when calculating allele counts, or does it count raw reads?If UMIs are not explicitly used for deduplication, what internal statistical mechanisms (e.g., the Bayesian model or genotype probability) are in place to prevent PCR bias from inflating the ASE signals?