RseqFlow: workflows for RNA-Seq data analysis | Zendy

Ying Wang | Zendy; Gaurang Mehta | Zendy; Rajiv Mayani | Zendy; Jingxi Lu | Zendy; Tade Souaiaia | Zendy; Yangho Chen | Zendy; Andrew P. Clark | Zendy; Hee Jae Yoon | Zendy; Lin Wan | Zendy; Oleg V. Evgrafov | Zendy; James A. Knowles | Zendy; Ewa Deelman | Zendy; Ting Chen | Zendy

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RseqFlow: workflows for RNA-Seq data analysis

Author(s) -

Ying Wang,

Gaurang Mehta,

Rajiv Mayani,

Jingxi Lu,

Tade Souaiaia,

Yangho Chen,

Andrew P. Clark,

Hee Jae Yoon,

Lin Wan,

Oleg V. Evgrafov,

James A. Knowles,

Ewa Deelman,

Ting Chen

Publication year - 2011

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btr441

Subject(s) - workflow , rna seq , computer science , computational biology , rna , software , database , transcriptome , programming language , biology , genetics , gene expression , gene

We have developed an RNA-Seq analysis workflow for single-ended Illumina reads, termed RseqFlow. This workflow includes a set of analytic functions, such as quality control for sequencing data, signal tracks of mapped reads, calculation of expression levels, identification of differentially expressed genes and coding SNPs calling. This workflow is formalized and managed by the Pegasus Workflow Management System, which maps the analysis modules onto available computational resources, automatically executes the steps in the appropriate order and supervises the whole running process. RseqFlow is available as a Virtual Machine with all the necessary software, which eliminates any complex configuration and installation steps.

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