Meeting Abstract

S4-1.4  Saturday, Jan. 5  RNA-seq for ecologists – fundamentals and practicalities WHEAT, Christopher W; Univ. of Helsinki, Finland chris@christopherwheat.net

Recent advances in DNA sequencing now provide unprecedented access to the transcriptome of any species. However, extracting informative quantitative expression insights is challenging, especially for the ecological researcher. Why? 1) The studied organism is not likely to have a well assembled genome or the gene models needed by many software programs for mapping RNA seq reads. Although the transcriptome can be assembled and used as a scaffold for mapping, generating a high quality transcritpome is a very challenging endeavor. 2) Researchers are likely to be focused upon complex phenotypes arising from expression variation that is much weaker than disease phenotypes such as cancer, etc., necessitating statistical approaches that leverage functional information. 3) Obtaining functional annotation is challenging, especially in the context of gene family dynamics and alternative splicing. During my presentation I will address each of the 3 issues, using data from butterflies to humans to illustrate these points and how steps can be taken to circumvent them.