Improved RNA-seq Workflows Using CyVerse Cyberinfrastructure.

Autor: Chougule KM; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York., Wang L; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York., Stein JC; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York., Wang X; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York., Devisetty UK; CyVerse, BIO5, University of Arizona, Tucson, Arizona., Klein RR; United States Department of Agriculture-Agriculture Research Service, Southern Plains Agricultural Research Center, College Station, Texas., Ware D; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.; United States Department of Agriculture-Agriculture Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York.
Jazyk: angličtina
Zdroj: Current protocols in bioinformatics [Curr Protoc Bioinformatics] 2018 Sep; Vol. 63 (1), pp. e53. Date of Electronic Publication: 2018 Aug 31.
DOI: 10.1002/cpbi.53
Abstrakt: RNA-seq is a vital method for understanding gene structure and expression patterns. Typical RNA-seq analysis protocols use sequencing reads of length 50 to 150 nucleotides for alignment to the reference genome and assembly of transcripts. The resultant transcripts are quantified and used for differential expression and visualization. Existing tools and protocols for RNA-seq are vast and diverse; given their differences in performance, it is critical to select an analysis protocol that is scalable, accurate, and easy to use. Tuxedo, a popular alignment-based protocol for RNA-seq analysis, has been updated with HISAT2, StringTie, StringTie-merge, and Ballgown, and the updated protocol outperforms its predecessor. Similarly, new pseudo-alignment-based protocols like Kallisto and Sleuth reduce runtime and improve performance. However, these tools are challenging for researchers lacking command-line experience. Here, we describe two new RNA-seq analysis protocols, in which all tools are deployed on CyVerse Cyberinfrastructure with user-friendly graphical user interfaces, and validate their performance using plant RNA-seq data. © 2018 by John Wiley & Sons, Inc.
(© 2018 John Wiley & Sons, Inc.)
Databáze: MEDLINE
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