NDLI: RNA-seq gene and transcript expression analysis using the BioExtract server and iPlant collaborative

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RNA-seq gene and transcript expression analysis using the BioExtract server and iPlant collaborative

Content Provider	ACM Digital Library
Author	Lushbough, Carol M. Gnimpieba, Etienne Z. Chango, Abalo
Abstract	Background: The development of Next Generation Sequencing (NGS) technology provides great opportunities to study gene expression, gene spliced transcripts, post-transcriptional changes, and gene fusion mutations/SNPs. The large amount of data being generated from these approaches presents many challenges. For example, how can we manage and analyze these vast datasets in order to extract new knowledge. Aims: This paper provides an integrated, adaptable, and scalable scenario to guide researchers through a complex, data analysis process using the iPlant Collaborative AGAVE RESTful API through the BioExtract Server. In 3 modules, we show how a High Performance Cluster (HPC) can be leveraged in a Workflow Management System (WMS) by following simple analytic steps. Results: A workflow has been developed in the BioExtract Server to analyze RNA-Seq data. The running of this workflow on a 21.6GB dataset provides reliable gene and transcript expression results. The BioExtract Server's results compared to an existing manual workflow on the same dataset shows ≈800% improvement in execution time (from ≈18h to ≈2h10min). Additionally, there are several qualitative improvements such as; automation, reproducibility, sharability, and scalability. (Note: the performance was not compared to the workflow installed at Galaxy, https://usegalaxy.org/, due to extensive wait times on their public site.) Our workflow execution provides analysis results from input datasets and reveals a 0.05 fold discovery rate (FDR) showing that 342 genes, 228 isoforms, 270 TSS, 47 CDS and 23 promoters are significantly differentially expressed. Conclusion: Having the ability to easily create and execute workflows leveraging the robust iPlant cyberinfrastructure to analyze NGS data represents one more steps in eScience initiative improvement. It improves, considerably, the ability of life science researchers to apply NGS tools. However, enhancements to this approach remains important as everyday improvements in HPC and WMS technology, techniques, and software continues. Our coming challenge will consist to follow that evolution in order to minimize the gap between researchers and these powerful resources. Availability: Tools used here are freely available on referenced link. Additional data analysis from our workflow execution is available on demand. Our workflow is available on MyExperiment under creative commons (cc) license (http://www.myexperiment.org/workflows/3895.html?version=1).
Starting Page	661
Ending Page	669
Page Count	9
File Format	PDF
ISBN	9781450328944
DOI	10.1145/2649387.2660822
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2014-09-20
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Workflow management system Rnaseq High performance computing Cyberinfrastructure Iplant collaborative Ngs Escience Bioextract
Content Type	Text
Resource Type	Article

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