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18 lines
898 B
Text
18 lines
898 B
Text
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Cufflinks assembles transcripts, estimates their abundances, and tests
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for differential expression and regulation in RNA-Seq samples. It
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accepts aligned RNA-Seq reads and assembles the alignments into a
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parsimonious set of transcripts. Cufflinks then estimates the relative
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abundances of these transcripts based on how many reads support each
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one, taking into account biases in library preparation protocols.
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Cufflinks is a collaborative effort between the Laboratory for
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Mathematical and Computational Biology, led by Lior Pachter at UC
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Berkeley, Steven Salzberg's computational genomics group at the
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Institute of Genetic Medicine at Johns Hopkins University, and Barbara
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Wold's lab at Caltech.
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Reference:
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Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer and
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Barbara Wold, "Mapping and quantifying mammalian transcriptomes by
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RNA-Seq", Nature Methods, volume 5, 621 - 628 (2008)
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