NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data
Eliah Overbey, Amanda Saravia-Butler, Zhe Zhang, Komal S. Rathi, Homer Fogle, Willian A. da Silveira, Richard Barker, Joseph J. Bass, Afshin Beheshti, Daniel C. Berrios, Elizabeth A. Blaber, Egle Cekanaviciute, Helio A. Costa, Laurence Davin, Kathleen M. Fisch, Samrawit Gebre, Matthew Geniza, Rachel Gilbert, Simon Gilroy, Gary Hardiman, Raúl Herranz, Yared H. Kidane, Colin P. S. Kruse, Michael Lee, Ted Liefeld, Norman Lewis, J. Tyson McDonald, Robert Meller, Tejaswini Mishra, Imara Y. Perera, Shayoni Ray, Sigrid Reinsch, Sara Brin Rosenthal, Michael Strong, Nathaniel J. Szewczyk, Candice Tahimic, Deanne Taylor, Joshua P. Vandenbrink, Alicia Villacampa, Silvio Weging, Chris Wolverton, Sarah E. Wyatt, Luis Zea, Sylvain V. Costes, Jonathan M. Galazka
Abstract
With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping, and gene quantification steps, culminating in the detection of differentially expressed genes. This data analysis pipeline and the results of its execution using data submitted to GeneLab are now all publicly available through the GeneLab database. We present here the full details and rationale for the construction of this pipeline in order to promote transparency, reproducibility, and reusability of pipeline data; to provide a template for data processing of future spaceflight-relevant datasets; and to encourage cross-analysis of data from other databases with the data available in GeneLab.