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=== RNA-Seq data analysis ===
RNA-Seq experiments generate a large volume of raw sequence reads which have to be processed to yield useful information. Data analysis usually requires a combination of [[List of open-source bioinformatics software|bioinformatics software]] tools (see also [[List of RNA-Seq bioinformatics tools]]) that vary according to the experimental design and goals. The process can be broken down into four stages: quality control, alignment, quantification, and differential expression.<ref name="#23481128">{{cite journal | vauthors = Van Verk MC, Hickman R, Pieterse CM, Van Wees SC | title = RNA-Seq: revelation of the messengers | journal = Trends in Plant Science | volume = 18 | issue = 4 | pages = 175–9 | date = April 2013 | pmid = 23481128 | doi = 10.1016/j.tplants.2013.02.001 | hdl = 1874/309456 | s2cid = 205453732 | hdl-access = free }}</ref> Most popular RNA-Seq programs are run from a [[command-line interface]], either in a [[Unix]] environment or within the [[R (programming language)|R]]/[[Bioconductor]] statistical environment.<ref name="#25633503">{{cite journal | vauthors = Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M | display-authors = 6 | title = Orchestrating high-throughput genomic analysis with Bioconductor | journal = Nature Methods | volume = 12 | issue = 2 | pages = 115–21 | date = February 2015 | pmid = 25633503 | pmc = 4509590 | doi = 10.1038/nmeth.3252 }}</ref>
==== Quality control ====
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