Question: RNA-Seq quantification of a heterozygous individual with a short deletion
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gravatar for elsoja
12 months ago by
elsoja120
elsoja120 wrote:

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

rna-seq • 257 views
ADD COMMENTlink modified 12 months ago by Lior Pachter540 • written 12 months ago by elsoja120
2
gravatar for Lior Pachter
12 months ago by
Lior Pachter540
United States
Lior Pachter540 wrote:

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

ADD COMMENTlink written 12 months ago by Lior Pachter540
1

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.

ADD REPLYlink written 12 months ago by elsoja120
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