RNA-Seq quantification of a heterozygous individual with a short deletion

Question

[Antonio Camargo]

I'm quantifying transcript expression of RNA-Seq data collected from a mouse that is heterozygous in a given locus. One of the alleles is wild-type while the other has a deletion (~20bp). Should I take any special care when quantifying those samples or can I use Salmon/Kallisto/RSEM with a standard GENCODE reference?

Thanks

Answer 1

[Lior Pachter]

You should modify your transcriptome to include both haplotypes for the gene.

[Antonio Camargo]

Thank you, Lior!

That's what I'm doing right now. I was apprehensive in introducing more ambiguity into a locus in which the individual isoform expression is a relevant information. However, it seems like the EM gave me results that are very close to what I was expecting.