NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data

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.

Daniel C. Berrios | Michael D. Lee | Afshin Beheshti | Homer Fogle | Nathaniel J Szewczyk | Ted Liefeld | Richard J. Barker | Michael Strong | Gary Hardiman | Sara Brin Rosenthal | Willian A. da Silveira | Amanda M. Saravia-Butler | Jonathan M. Galazka | Elizabeth A. Blaber | Luis Zea | Sylvain V. Costes | Samrawit G Gebre | Norman G. Lewis | Simon Gilroy | Kathleen M. Fisch | Sigrid S. Reinsch | Helio A. Costa | Willian A. da Silveira | Raúl Herranz | Eliah G. Overbey | Zhe Zhang | Komal S. Rathi | Joseph J. Bass | Egle Cekanaviciute | Laurence B. Davin | Samrawit G. Gebre | Matthew Geniza | Rachel Gilbert | Yared H. Kidane | Colin P.S. Kruse | J. Tyson McDonald | Robert Meller | Tejaswini Mishra | Imara Y. Perera | Shayoni Ray | Candice G.T. Tahimic | Deanne M. Taylor | Joshua P. Vandenbrink | Alicia Villacampa | Silvio Weging | Chris Wolverton | Sarah E. Wyatt | Deanne M. Taylor | T. Liefeld | Michael D. Lee | G. Hardiman | S. Rosenthal | L. Davin | N. Lewis | Matthew J. Geniza | D. Berrios | Richard Barker | A. Beheshti | W. D. da Silveira | Egle Cekanaviciute | C. Tahimic | E. Blaber | J. McDonald | S. Costes | S. Wyatt | Joshua P Vandenbrink | R. Herranz | M. Strong | R. Meller | Tejaswini Mishra | S. Reinsch | K. Fisch | S. Gilroy | N. Szewczyk | K. Rathi | L. Zea | J. Galazka | Shayoni Ray | Zhe Zhang | I. Perera | Samrawit Gebre | C. Wolverton | J. Bass | Rachel Gilbert | Alicia Villacampa | Colin P. S. Kruse | Homer Fogle | Silvio Weging | Matthew Geniza | Deanne M. Taylor | Afshin Beheshti | Joshua Vandenbrink | S. Weging | Eliah G Overbey

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