Hi all,
I'm pleased to let you know that I've recently released a new tool for analyzing RNA-Seq data that you may find useful. The program, Cufflinks, is designed to assemble the transcripts in an RNA-Seq sample and calculate their abundances (in transcript-level RPKM). Cufflinks is built to work without a reference annotation. You need only a reference genome and an input file of RNA-Seq read alignments (in SAM format), such as the one produced by TopHat.
Cufflinks currently supports only Mac OS X and Linux, and you'll need a medium-sized machine to run it. The program is fast and fully threaded, but for large (>100 million aligned reads) runs, the memory footprint can be 10GB or more.
This is only the first release, and there are numerous features planned for the next weeks and months. The project is a collaboration between scientists at the University of Maryland, UC Berkeley, Caltech, and WashU. We would be grateful for any feedback, suggestions, bug reports, or criticism you have. We hope you find Cufflinks useful.
I'm pleased to let you know that I've recently released a new tool for analyzing RNA-Seq data that you may find useful. The program, Cufflinks, is designed to assemble the transcripts in an RNA-Seq sample and calculate their abundances (in transcript-level RPKM). Cufflinks is built to work without a reference annotation. You need only a reference genome and an input file of RNA-Seq read alignments (in SAM format), such as the one produced by TopHat.
Cufflinks currently supports only Mac OS X and Linux, and you'll need a medium-sized machine to run it. The program is fast and fully threaded, but for large (>100 million aligned reads) runs, the memory footprint can be 10GB or more.
This is only the first release, and there are numerous features planned for the next weeks and months. The project is a collaboration between scientists at the University of Maryland, UC Berkeley, Caltech, and WashU. We would be grateful for any feedback, suggestions, bug reports, or criticism you have. We hope you find Cufflinks useful.
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