A manual update of genomic annotations improves isoform quantifications

What is it about?

Quantification software are powerful tools to rapidly quantify isoform usage in RNA-seq experiments. As they rely solely on annotated gene models, they can be subject to biases when such annotations are inaccurate. Through the example of the Khk gene in mouse, we provide an example of such biases and show that they can be overcome when genomic annotations are adequately updated. We also confirm our computational estimations using RT-qPCR.

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Why is it important?

Our findings show that it is important to consider the accuracy of genomic annotations when quantifying isoform using RNA-seq. As estimates might be biased, we recommend to thoroughly validate any unexpected findings with orthogonal methods.

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