Differential Gene and Transcript Expression Analysis with TopHat and Cufflinks

ABSTRACT: This submission includes the sample data for a protocol covering differential expression analysis with TopHat and Cufflinks. The protocol also covers several accessory tools and utilities that aid in managing data, including CummeRbund, a tool for visualizing RNA-Seq analysis results. While 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 example data was generated in silico to closely resemble a real experiment in Drosophila melanogaster. First, expression values i

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Cole Trapnell 

PROVIDER: E-GEOD-32038 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress