Studying oogenesis in a non-model organism using transcriptomics: assembling, annotating, and analysing your data

Carter, Jean-Michel; Gibbs, Melanie ORCID: https://orcid.org/0000-0002-4091-9789; Breuker, Casper J.. 2016 Studying oogenesis in a non-model organism using transcriptomics: assembling, annotating, and analysing your data. In: Nezis, Ioannis P., (ed.) Oogenesis: methods and protocols. New York, Humana Press, 129-143. (Methods in Molecular Biology, 1457).

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Abstract/Summary

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.

Item Type:	Publication - Book Section
Digital Object Identifier (DOI):	10.1007/978-1-4939-3795-0_10
UKCEH and CEH Sections/Science Areas:	Pywell
ISBN:	9781493937936
Additional Keywords:	transcriptome, de-novo assembly, annotation, non-model organism, oogenesis
NORA Subject Terms:	Ecology and Environment Zoology
Date made live:	20 Sep 2016 11:14 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/514502

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