… (c) For a gene with two expressed isoforms, exons are colored according to the isoform of …
Trapnell, C. et al. Transcript assembly and quantification by RNA-seq reveals unannotated …

A revolution in cellular measurement technology is under way: For the first time, we have
the ability to monitor global gene regulation in thousands of individual cells in a single …

… Cole Trapnell … Cole Trapnell and Steven L. Salzberg are at the Center for
Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland …

… (a) When abundances of isoforms A, B and C of Myc are grouped by TSS, changes in the …
(c) Myc isoforms are downregulated as the time course proceeds. The width of the colored …

… In the version of this article initially published, the computer script in Box 1 sections B and C,
and in Procedure Step 1, contained errors: the last section of the final three lines of the script …

Motivation: A new protocol for sequencing the messenger RNA in a cell, known as RNA-Seq,
generates millions of short sequence fragments in a single run. These fragments, or ‘reads’…

Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence
reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie …

TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper,
we describe TopHat2, which incorporates many significant enhancements to TopHat. …

… , dissociated cells were captured and processed with the C 1 Single-Cell Auto Prep System
(… are captured in each C 1 microfluidic device. In this study, we used one C 1 capture chip at 0…

… (c) Methods for performing differential gene expression analysis with RNA-seq based on the
exon-union counting method returned nearly all of the genes returned by Cuffdiff 2. (d) Lung …