Quantification of allele-specific gene expression in RNA-seq

Question

[Petesview]

Hi Bioinformaticians,

Sorry for a naive question which I couldn't find an answer to online.

If an individual has two alleles for a given gene hence these are SNP variants, then during RNA-seq analysis, are the expression of both alleles quantified together and assigned to a single gene symbol? Or are they separated quantified, and that there are corresponding gene symbols for each variant in the GTF file?

Thanks for your help.

[biofalconch]

There are a few threads here on this topic like this one: Allele Specific Expression Analysis :)

[Petesview]

Thanks for the guidance. I'm just curious whether expression of the two alleles for a gene is quantified together in a conventional RNA-seq analysis. I don't necessarily want need to perform allele specific expression analysis.

[biofalconch]

I'm just curious whether expression of the two alleles for a gene is quantified together in a conventional RNA-seq analysis

Yes, they are quantified under the same gene, you would need specific tools like ASEReadCounter to quantify allele specific expression, as the GTF only contains genomic coordinates and not variant information.

[Petesview]

Thank you! Also, if a gene is duplicated, does that mean it would share the same gene symbol, but have a different ID? Thus the gene ID differentiates the coordinates of the duplicated gene?

Answer 1

[i.sudbery]

The answer to this question will depend on the analysis method. But most default methods don't distinguish between alleles of sequence. In pretty much all cases reference genome sequences (and therefore annotation GTFs) assume the genome is haploid, and has only one sequence. There are no standard ways to refer to specific alleles in reference genome sequences or reference GTFs.

[Petesview]

Thanks for the response. This makes a lot of sense.