20 lines
963 B
Plaintext
20 lines
963 B
Plaintext
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.
|
|
|
|
NOTE: This just repackages the binaries provided from upstream.
|
|
|
|
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)
|