Major advances in sequencing technology have contributed to the ability to examine complex patterns of genome activity in a wide range of organisms that are extensively used for comparative physiology, ecology and evolution, environmental monitoring, and commercial aquaculture. Relative to insect and vertebrate model organisms, however, information on the organization of crustacean genomes is virtually nonexistent, making de novo transcriptome assembly, annotation and quantification problematic and challenging.
Researchers from Colorado State University and the University of Oklahoma present a summary of the methodologies and software analyses employed in 23 recent publications, which describe de novo transcriptome assembly, annotation, and differential gene expression in a variety of crustacean experimental systems. They focus on establishing a series of best practices that will allow for investigators to produce datasets that are understandable, reproducible, and of general utility for related analyses and cross-study comparisons.
Analytical pipeline for RNA-seq data analysis
This pipeline encompasses an overall data analysis method that results in identification of differentially expressed (DE) transcripts, followed by enriched Gene Ontologies (GO) and pathways, and DE transcripts with similar expression profiles (see text for details). The most commonly used tools for this pipeline are listed in the text.