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Transcript identification and the quantification of gene expression have been distinct core activities in molecular biology ever since the discovery of RNA’s role as the key intermediate between the genome and the proteome. Scientists plan experiments and adopt different analysis strategies depending on the organism being studied and their research goals. For example, if a genome sequence is available for the studied organism, it should be possible to identify transcripts by mapping RNA-seq reads onto the genome.
(Conesa et al., 2016) A survey of best practices for RNA-seq data analysis. Genome Biology.