Computational tool evaluation demonstrates accurate transcript quantification from RNA-Seq data without reference genomes, suggesting cost-effective experimental sequencing design.
RSEM is an accurate and user-friendly software tool for quantifying transcript abundances from RNA-Seq data. As it does not rely on the existence of a reference genome, it is particularly useful for quantification with de novo transcriptome assemblies. In addition, RSEM has enabled valuable guidance for cost-efficient design of quantification experiments with RNA-Seq, which is currently relatively expensive.
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Li et al. (2011) studied this question.
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