I'm very pleased to announce that the paper describing Cufflinks has appeared at Nature Biotechnology. Those interested in the algorithms and mathematics in the Cufflinks package will want to look at the Supplemental Methods (warning, large PDF). The abstract for the paper is attached.
Sincerely,
Cole Trapnell
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Cole Trapnell, Brian A. Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J. van Baren, Steven L. Salzberg, Barbara J. Wold, and Lior Pachter
High-throughput mRNA sequencing (RNA-Seq) promises simultaneous transcript discovery and abundance estimation. However, this would require algorithms that are not restricted by prior gene annotations and that account for alternative transcription and splicing. Here we introduce such algorithms in an open-source software program called Cufflinks. To test Cufflinks, we sequenced and analyzed >430 million paired 75-bp RNA-Seq reads from a mouse myoblast cell line over a differentiation time series. We detected 13,692 known transcripts and 3,724 previously unannotated ones, 62% of which are supported by independent expression data or by homologous genes in other species. Over the time series, 330 genes showed complete switches in the dominant transcription start site (TSS) or splice isoform, and we observed more subtle shifts in 1,304 other genes. These results suggest that Cufflinks can illuminate the substantial regulatory flexibility and complexity in even this well-studied model of muscle development and that it can improve transcriptome-based genome annotation.
(cross posted from the Bowtie announcements mailing list, apologies to those who have seen this already)
Sincerely,
Cole Trapnell
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Cole Trapnell, Brian A. Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J. van Baren, Steven L. Salzberg, Barbara J. Wold, and Lior Pachter
High-throughput mRNA sequencing (RNA-Seq) promises simultaneous transcript discovery and abundance estimation. However, this would require algorithms that are not restricted by prior gene annotations and that account for alternative transcription and splicing. Here we introduce such algorithms in an open-source software program called Cufflinks. To test Cufflinks, we sequenced and analyzed >430 million paired 75-bp RNA-Seq reads from a mouse myoblast cell line over a differentiation time series. We detected 13,692 known transcripts and 3,724 previously unannotated ones, 62% of which are supported by independent expression data or by homologous genes in other species. Over the time series, 330 genes showed complete switches in the dominant transcription start site (TSS) or splice isoform, and we observed more subtle shifts in 1,304 other genes. These results suggest that Cufflinks can illuminate the substantial regulatory flexibility and complexity in even this well-studied model of muscle development and that it can improve transcriptome-based genome annotation.
(cross posted from the Bowtie announcements mailing list, apologies to those who have seen this already)
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