Cufflinks¶
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.
Details¶
References¶
Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms.
C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M.J. van Baren, S.L. Salzberg, B.J. Wold, L. Pachter.
Nature Biotechnology (2010) 28, 511–515