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Of contigs and quagmires: next‐generation sequencing pitfalls associated with transcriptomic studies
Author(s) -
DeWoody J. Andrew,
Abts Kendra C.,
Fahey Anna L.,
Ji Yanzhu,
Kimble Steven J. A.,
Marra Nicholas J.,
Wijayawardena Bhagya K.,
Willoughby Janna R.
Publication year - 2013
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12107
Subject(s) - biology , dna sequencing , computational biology , transcriptome , contig , data science , ecology , microbiology and biotechnology , genetics , genome , dna , computer science , gene , gene expression
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.