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.
Perspectives
We hope that this work will help improve the current bioinformatics tools used to estimate isoform quantifications from RNA-seq.
Christophe Chabbert
ETH Zürich
Read the Original
This page is a summary of: Correction of gene model annotations improves isoform abundance estimates: the example of ketohexokinase (Khk), F1000Research, December 2018, Faculty of 1000, Ltd.,
DOI: 10.12688/f1000research.17082.1.
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Extended Data
The extended data provides important additional data and visualisation supporting the findings of the study.
Underlying Data
The underlying data contains important files (annotations, primers) used in this study.
Code
This git repository contains the code used to generate the analysis of this study.
Contributors
The following have contributed to this page
