RseqFlow: Workflows for RNA-Seq data analysis

Ying Wang, 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

Research output: Contribution to journalArticlepeer-review

22 Scopus citations

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.

Original languageEnglish (US)
Article numberbtr441
Pages (from-to)2598-2600
Number of pages3
JournalBioinformatics
Volume27
Issue number18
DOIs
StatePublished - Sep 2011
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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