ARS | Publication request: Effects of incomplete reference transcriptomes on RNA-Seq mapping for higher eukaryotes

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: May 15, 2012
Publication Date: N/A

Technical Abstract: Whole transcriptome sequencing using next generation sequencing (NGS) technologies or RNA sequencing (RNA-Seq) has been growing in popularity for studying nonmodel organisms in the fields of agriculture, evolution, and medicine. With NGS technology evolving to the point where the cost is within the budgetary range of many funding agencies and the resultant data mineable for a range of applications, an increasing number of labs are chosing RNA-Seq for their research. However, many of the computational tools were developed for model organisms for which a complete reference transcriptome is available. In this study, we use simulations of real transcriptomes (from the Ensembl database) with 1% random substitution error and 100 bp single-end reads to assess the accuracy of current RNA-Seq mapping tools when applied to data from organisms that do not have a complete reference transcriptome.