[PMID:27107712] [Genome Biology]

A benchmark for RNA-seq quantification pipelines

“Note that for the ROC analysis we show results for both gene level and transcript level analysis and the transcript level metrics were substantially worse. Previous publications [PMID:26201343] focusing on abundance found that all algorithms performed well. Here we found that if your focus is differential expression, then results are not as impressive and differences are found across algorithms.””Finally, note that our method is meant to assess the quantification method specifically. Because, in general, our method does not consider biological replicates, it is not meant to be used for comparisons of statistical methods such as DESeq2 and edgeR.”


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