Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2011 Sep 15;27(18):2598-600.
doi: 10.1093/bioinformatics/btr441. Epub 2011 Jul 27.

RseqFlow: workflows for RNA-Seq data analysis

Ying Wang  1 , Gaurang Mehta, Rajiv Mayani, Jingxi Lu, Tade Souaiaia, Yangho Chen, Andrew Clark, Hee Jae Yoon, Lin Wan, Oleg V Evgrafov, James A Knowles, Ewa Deelman, Ting Chen
Affiliations

RseqFlow: workflows for RNA-Seq data analysis

Ying Wang et al. Bioinformatics. .

Abstract

Summary: 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.

Availability and implementation: http://genomics.isi.edu/rnaseq

Contact: wangying@xmu.edu.cn; knowles@med.usc.edu; deelman@isi.edu; tingchen@usc.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

PubMed Disclaimer

References

    1. Anders S., Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11:R106. - PMC - PubMed
    1. Callaghan S., et al. Scaling up workflow-based applications. J. Comput. Syst. Sci. 2010;76:428–446.
    1. Chen Y., et al. PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Bioinformatics. 2009;25:2514–2521. - PMC - PubMed
    1. Deelman E., et al. Pegasus: a framework for mapping complex scientific workflows onto distributed systems. Sci. Program. J. 2005;13:219–237.
    1. Deelman E., et al. Workflows for e-Science. London: Springer; 2007. Pegasus: mapping large-scale workflows to distributed resources; pp. 376–394. Part III.

Publication types