Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.

Resource Type: 
Publication
Publication Type: 
Journal Article
Title: 
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Authors: 
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L
Series Name: 
Nature protocols
Journal Abbreviation: 
Nat Protoc
Volume: 
7
Issue: 
3
Page Numbers: 
562-78
Publication Year: 
2012
Publication Date: 
2012 Mar 01
DOI: 
10.1038/nprot.2012.016
ISSN: 
1750-2799
EISSN: 
1750-2799
Cross Reference: 
PMIDLoading content
Citation: 
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.. Nature protocols. 2012 Mar 01; 7(3):562-78.
Abstract: 

Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes and splice variants and quantify expression genome-wide in a single assay. The volume and complexity of data from RNA-seq experiments necessitate scalable, fast and mathematically principled analysis software. TopHat and Cufflinks are free, open-source software tools for gene discovery and comprehensive expression analysis of high-throughput mRNA sequencing (RNA-seq) data. Together, they allow biologists to identify new genes and new splice variants of known ones, as well as compare gene and transcript expression under two or more conditions. This protocol describes in detail how to use TopHat and Cufflinks to perform such analyses. It also covers several accessory tools and utilities that aid in managing data, including CummeRbund, a tool for visualizing RNA-seq analysis results. Although the procedure assumes basic informatics skills, these tools assume little to no background with RNA-seq analysis and are meant for novices and experts alike. The protocol begins with raw sequencing reads and produces a transcriptome assembly, lists of differentially expressed and regulated genes and transcripts, and publication-quality visualizations of analysis results. The protocol's execution time depends on the volume of transcriptome sequencing data and available computing resources but takes less than 1 d of computer time for typical experiments and ∼1 h of hands-on time.

Publication Model: 
Electronic
Language: 
English
Language Abbr: 
eng
Journal Country: 
England