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RNA-seq is widely used to determine differential expression of genes or transcripts as well as identify novel transcripts, identify allele-specific expression, and precisely measure translation of transcripts. Thoughtful experimental design and choice of analysis tools are critical to ensure high-quality data and interpretable results. Important considerations for experimental design include number of replicates, whether to collect paired-end or single-end reads, sequence length, and sequencing depth.
(Williamset al., 2014) RNA-seq Data: Challenges in and Recommendations for Experimental Design and Analysis. Curr Protoc Hum Genet.