De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.

ABSTRACT: De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol we describe the use of the Trinity platform for de novo transcriptome assembly from RNA-seq data in non-model organisms. We also present Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes. In the procedure, we provide a workflow for genome-independent transcriptome analysis leveraging the T

SUBMITTER: Haas BJ 

PROVIDER: S-EPMC3875132 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature