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

• Published in: Molecular ecology resources 2013-07, Vol.13 (4), p.551-558
• Main Authors: DeWoody, J. Andrew, Abts, Kendra C., Fahey, Anna L., Ji, Yanzhu, Kimble, Steven J. A., Marra, Nicholas J., Wijayawardena, Bhagya K., Willoughby, Janna R.
• Format: Article
• Language: English
• Subjects: Animal and plant ecology; Animal, plant and microbial ecology; Biological and medical sciences; Computational Biology - methods; DNA Contamination; Fundamental and applied biological sciences. Psychology; General aspects; Genetics of eukaryotes. Biological and molecular evolution; genomics; High-Throughput Nucleotide Sequencing - methods; High-Throughput Nucleotide Sequencing - standards; Illumina; next-generation sequencing; Population genetics, reproduction patterns; RNA-seq; Studies; Synecology; Transcriptome; transcriptomics
• ISSN: 1755-098X; 1755-0998
• DOI: 10.1111/1755-0998.12107

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.