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Blind spots of quantitative RNA-seq: The limits for assessing abundance, differential expression, and isoform switching

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RNA-seq is now widely used to quantitatively assess gene expression, expression differences and isoform switching, and promises to deliver results for the entire transcriptome. However, whether the transcriptional state of a gene can be captured accurately depends critically on library preparation, read alignment, expression estimation and the tests for differential expression and isoform switching. |