WebCufflinks. A transcript assembler and abundance estimator for RNA-seq data. Cufflinks assembles transcripts from the alignments produced by TopHat, including novel isoforms, and quantitates those transcripts. Cufflinks was originally developed by Cole Trapnell and is supported by his lab at the University of Washington. http://cole-trapnell-lab.github.io/cufflinks/how_it_works/
Bioconductor - cummeRbund
WebJul 23, 2015 · Here we develop a single-cell universal poly (A)-independent RNA sequencing (SUPeR-seq) method to sequence both polyadenylated and non-polyadenylated RNAs from individual cells. This method exhibits robust sensitivity, precision and … WebThere are several different tools available for RNA-Seq analysis. One of the more popular tools is Cufflinks, a all-in-one tool for performing several aspects of RNA-Seq analysis. One of Cufflinks' best features is that it can function as a reference-based de novo transcriptome assembler - that is, it can identify novel transcripts in your ... brookfield la trobe financial
Analysis of RNA-Seq Data Using TopHat and Cufflinks
WebFeb 18, 2015 · Using a network flow algorithm from optimization theory enables improved assembly of transcriptomes from RNA-seq reads. Methods used to sequence the transcriptome often produce more than 200 ... WebCufflinks. #What is Cufflinks? #How does Cufflinks assemble transcripts? #How does Cufflinks calculate transcript abundances? #How does Cufflinks estimate the fragment length distribution? #How does Cufflinks identify and correct for sequence bias? #How does Cufflinks handle multi-mapped reads? #How does Reference Annotation Based … WebCufflinks Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. brookfield landscape maintenance reviews