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diff --git a/academic/cufflinks/README b/academic/cufflinks/README new file mode 100644 index 0000000000..7afb95ee6e --- /dev/null +++ b/academic/cufflinks/README @@ -0,0 +1,17 @@ +Cufflinks assembles transcripts, estimates their abundances, and tests +for differential expression and regulation in RNA-Seq samples. It +accepts aligned RNA-Seq reads and assembles the alignments into a +parsimonious set of transcripts. Cufflinks then estimates the relative +abundances of these transcripts based on how many reads support each +one, taking into account biases in library preparation protocols. + +Cufflinks is a collaborative effort between the Laboratory for +Mathematical and Computational Biology, led by Lior Pachter at UC +Berkeley, Steven Salzberg's computational genomics group at the +Institute of Genetic Medicine at Johns Hopkins University, and Barbara +Wold's lab at Caltech. + +Reference: +Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer and +Barbara Wold, "Mapping and quantifying mammalian transcriptomes by +RNA-Seq", Nature Methods, volume 5, 621 - 628 (2008) |