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The simplest way to quantify genes is to check if a read’s location overlaps with the location of a gene. If it does, we assign the read to the overlapping gene.

In the image, Gene 1 (with eight reads mapped to it) is expressed at twice the level of Gene 2 (with four reads mapped to it). Researchers can then look at how these different gene expression levels affect the traits being studied. For example, how does higher expression of Gene 1 compared to Gene 2 affect your dog's risk of developing hip dysplasia, a hip joint structural problem?

The same challenges that apply to RNA-seq alignment can affect read quantification. A read can map to multiple genes, and you have to figure out which gene it really came from. RNA splicing can also make gene quantification challenging.