Of contigs and quagmires: next-generation sequencing pitfalls associated with transcriptomic studies.

Autor: DeWoody JA; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA. dewoody@purdue.edu, Abts KC, Fahey AL, Ji Y, Kimble SJ, Marra NJ, Wijayawardena BK, Willoughby JR
Jazyk: angličtina
Zdroj: Molecular ecology resources [Mol Ecol Resour] 2013 Jul; Vol. 13 (4), pp. 551-8. Date of Electronic Publication: 2013 Apr 25.
DOI: 10.1111/1755-0998.12107
Abstrakt: Molecular ecologists have good reasons to be excited about the newest DNA/RNA sequencing technologies. However, this exuberance should be tempered with a hefty dose of reality: new sequencing technologies come with significant new challenges. Herein, we offer a brief overview of some practical problems encountered during transcriptomics studies conducted in our laboratory, and of nontrivial issues that prospective practitioners should consider. These include template contamination (e.g. from xenobiotics) and the cutting-room floor problem, whereby most of the data are often unassembled, unannotated and unused. We also highlight computational requirements, including hardware, personnel time and associated skill sets. We are very optimistic about the future of molecular ecology, but we hope this cautionary overview will help neophytes better recognize some key challenges associated with new technologies.
(© 2013 John Wiley & Sons Ltd.)
Databáze: MEDLINE
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