title: Studying Oogenesis in a Non-model Organism Using Transcriptomics: Assembling, Annotating, and Analyzing Your Data.
abstract: This chapter provides a guide to processing and analyzing RNA-Seq data in a non-model organism. This approach was implemented for studying oogenesis in the Speckled Wood Butterfly Pararge aegeria. We focus in particular on how to perform a more informative primary annotation of your non-model organism by implementing our multi-BLAST annotation strategy. We also provide a general guide to other essential steps in the next-generation sequencing analysis workflow. Before undertaking these methods, we recommend you familiarize yourself with command line usage and fundamental concepts of database handling. Most of the operations in the primary annotation pipeline can be performed in Galaxy (or equivalent standalone versions of the tools) and through the use of common database operations (e.g. to remove duplicates) but other equivalent programs and/or custom scripts can be implemented for further automation.
authors.affiliation: Evolutionary Developmental Biology Research Group, Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Gipsy Lane, Headington, Oxford, OX3 0BP, UK.
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Carter
authors.affiliation: NERC Centre for Ecology & Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, UK.
authors.forename: Melanie
authors.initials: M
authors.lastname: Gibbs
authors.affiliation: Evolutionary Developmental Biology Research Group, Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Gipsy Lane, Headington, Oxford, OX3 0BP, UK. cbreuker@brookes.ac.uk.
authors.forename: Casper J
authors.initials: CJ
authors.lastname: Breuker
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling / Q000379:methods; D063990:Gene Ontology; D058977:Molecular Sequence Annotation; D009866:Oogenesis / Q000235:genetics*; D011786:Quality Control; D012984:Software; D059467:Transcriptome; D064878:Web Browser; D057188:Workflow
keywords: Annotation; De-novo assembly; Non-model organism; Oogenesis; Transcriptome