Question: Oarfish suitable for Quantifying Haplotype-Resolved Transcriptomes

[nadjano]

Hello,

I’m curious whether Oarfish can be applied to estimate counts from alignments to a diploid (or higher ploidy) transcriptome.

Is the EM model specifically designed to resolve ambiguities between isoforms, rather than distinguishing alleles of the same gene?

I assume that the statistics should be different if I want to get counts on the allele level (and not so interested in the isoform expression) and also expect to have similar transcripts from gene families or gene duplications.

Would you suggest using Oarfish for this purpose, or would it be better to explore other tools?

Thank you for your time and kind regards,
Nadja