Transcript assembly and quantification by RNA-Seq reveals.pdfVIP

l e t t e r s transcript assembly and quantification by rNA-seq reveals unannotated transcripts and isoform switching during cell differentiation 1–3 4 2 4 4 5 Cole Trapnell , Brian A Williams , Geo Pertea , Ali Mortazavi , Gordon Kwan , Marijke J van Baren , 1,2 4 3,6,7 Steven L Salzberg , Barbara J Wold Lior Pachter . d e High-throughput mRNA sequencing (RNA-Seq) promises (75 bp in this work versus 25 bp in our previous work) and pairs of v r simultaneous transcript discovery and abundance estimation1–3. reads from both ends of each RNA fragment can reduce uncertainty e s However, this would require algorithms that are not restricted in assigning reads to alternative splice variants12. To produce use- e r s by prior gene annotations and that account for alternative ful transcript-level abundance estimates from paired-end RNA-Seq t h transcription and splicing. Here we introduce such algorithms data, we developed a new algorithm that can identify complete novel g i in an open-source software program called Cufflinks. To test transcripts and probabilistically assign reads to isoforms. r l l Cufflinks, we sequenced and analyzed 430 million paired For our initial demonstration of Cufflinks, we performed a time A . 75-bp RNA-Seq reads from a mouse myoblast cell line over course of paired-end 75-bp RNA-Seq on a well-studied model of c n a differentiation time series. We detected 13,692 known