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Stem Cell Transcriptional Networks

Volume 1150 of the series Methods in Molecular Biology pp 21-43

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Analysis of Next-Generation Sequencing Data Using Galaxy

  • Daniel BlankenbergAffiliated withDepartment of Biochemistry and Molecular Biology, Penn State University Email author 
  • , Jennifer Hillman-JacksonAffiliated withDepartment of Biochemistry and Molecular Biology, Penn State University

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Abstract

The extraordinary throughput of next-generation sequencing (NGS) technology is outpacing our ability to analyze and interpret the data. This chapter will focus on practical informatics methods, strategies, and software tools for transforming NGS data into usable information through the use of a web-based platform, Galaxy. The Galaxy interface is explored through several different types of example analyses. Instructions for running one’s own Galaxy server on local hardware or on cloud computing resources are provided. Installing new tools into a personal Galaxy instance is also demonstrated.

Key words

NGS Genomics Informatics RNA-seq ChIP-seq Workflows Reproducibility Open source Web-based workbench Big data analysis