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Workflow of RNA-seq data analysis pipeline. The five dashed boxes correspond to five steps in the RNA-seq data analysis pipeline. We applied two alignment tools and two quantification tools to estimate gene/isoform expression with normalization methods of count, TPM, or FPKM. The fold-change method and the edgeR tool are used to infer differentially expressed genes. At each analysis step, we assess the variations resulting from genome annotation choice.
