RNA sequencing: the teenage years

By Rory Stark, Marta Grzelak, J. Hadfield. Nature reviews genetics, 2019

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PyDESeq2: a python package for bulk RNA-seq differential expression analysis (2022, methodology): “Most RNA-seq datasets are used primarily for di ↵ erential expression analysis (DEA) (Stark et al. , 2019) which provides invaluable insight on the associations between the genes’ expression and a phenotype.”
Improved transcriptome assembly using a hybrid of long and short reads with StringTie (2021, background): “These include the rapid rate of RNA degradation, shearing of the RNA during library preparation, or incomplete synthesis of cDNA [3].”
Next-Generation Sequencing Technology: Current Trends and Advancements (2023, methodology): “The various bioinformatics tools used in NGS analysis are listed in Table 3.”
A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines (2021, background): “(8) Detection and quantification of full length fusion transcripts The occurrence of genomic rearrangements in cancer can introduce fusion genes which are associated with clinical characteristics 30.”