Cufflinks

Transcript assembly and abundance estimation for RNA-Seq

Cufflinks assembles transcripts and estimates their abundances 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.

Cufflinks is a collaborative effort between the Laboratory for Mathematical and Computational Biology, led by Lior Pachter at UC Berkeley, Steven Salzberg's group at the University of Maryland Center for Bioinformatics and Computational Biology, and Barbara Wold's lab at Caltech.

Cufflinks is provided under the OSI-approved Boost License

Site Map

Releases

version 0.7.0 (BETA)	9/26/2009
Source code
Linux x86_64 binary
Mac OS X x86_64 binary

Related Tools

TopHat: Alignment of short RNA-Seq reads
Bowtie: Ultrafast short read alignment

Publications

(Cufflinks manuscript coming soon)
Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics doi:10.1093/bioinformatics/btp120
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.

Contributors

Cole Trapnell
Geo Pertea
Brian Williams
Ali Mortazavi
Jeltje van Baren
Steven Salzberg
Barbara Wold
Lior Pachter

0.7.0 release - 9/26/2009

The first public release of Cufflinks is now available for download. Cufflinks is a program for the comparative assembly of transcripts and the estimation of their abundances in an RNA-Seq experiment. It runs on Linux and OS X. It also comes with a tool to track transcripts across multiple samples, for example in a time course of RNA-Seq.

Cufflinks takes as input a file of alignments in SAM format, and reports transfrags in GTF format. You can use TopHat to align your reads, as TopHat reports its alignments in SAM format.

This software is a work in progress - it is a beta release, and new features will continue to be added over the next couple of weeks. To suggest a feature or report a bug, please email Cole Trapnell