title: OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid.
abstract: High-throughput DNA sequencing technology has revolutionized the study of gene expression while introducing significant computational challenges for biologists. These computational challenges include access to sufficient computer hardware and functional data processing workflows. Both these challenges are addressed with our scalable, open-source Pegasus workflow for processing high-throughput DNA sequence datasets into a gene expression matrix (GEM) using computational resources available to U.S.-based researchers on the Open Science Grid (OSG). We describe the usage of the workflow (OSG-GEM), discuss workflow design, inspect performance data, and assess accuracy in mapping paired-end sequencing reads to a reference genome. A target OSG-GEM user is proficient with the Linux command line and possesses basic bioinformatics experience. The user may run this workflow directly on the OSG or adapt it to novel computing environments.
authors: Department of Genetics and Biochemistry, Clemson University, SC, USA.
authors: William L
authors: WL
authors: Poehlman
authors: Information Sciences Institute, University of Southern California, Marina Del Rey, CA, USA.
authors: Mats
authors: M
authors: Rynge
authors: Center for Computation and Technology, Louisiana State University, Baton Rouge, LA, USA.
authors: Chris
authors: C
authors: Branton
authors: Computation Institute, University of Chicago, Chicago, IL, USA.
authors: D
authors: D
authors: Balamurugan
authors: Department of Genetics and Biochemistry, Clemson University, SC, USA.
authors: Frank A
authors: FA
authors: Feltus
keywords: DNA sequence analysis; Open Science Grid; Pegasus; RNAseq; distributed computing