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
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
Links
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

