title: Of contigs and quagmires: next-generation sequencing pitfalls associated with transcriptomic studies.
abstract: 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.
authors.affiliation: Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA. dewoody@purdue.edu
authors.forename: J Andrew
authors.initials: JA
authors.lastname: DeWoody
authors.forename: Kendra C
authors.initials: KC
authors.lastname: Abts
authors.forename: Anna L
authors.initials: AL
authors.lastname: Fahey
authors.forename: Yanzhu
authors.initials: Y
authors.lastname: Ji
authors.forename: Steven J A
authors.initials: SJ
authors.lastname: Kimble
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Marra
authors.forename: Bhagya K
authors.initials: BK
authors.lastname: Wijayawardena
authors.forename: Janna R
authors.initials: JR
authors.lastname: Willoughby
mesh_terms: D019295:Computational Biology / Q000379:methods*; D059018:DNA Contamination; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods* / Q000592:standards; D059467:Transcriptome