title: RseqFlow: workflows for RNA-Seq data analysis.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  http://genomics.isi.edu/rnaseq
  
  
  BACKGROUND
  wangying@xmu.edu.cn; knowles@med.usc.edu; deelman@isi.edu; tingchen@usc.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biological Sciences, USC, Los Angeles, CA 90089, USA. wangying@xmu.edu.cn
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.forename: Gaurang
authors.initials: G
authors.lastname: Mehta
authors.forename: Rajiv
authors.initials: R
authors.lastname: Mayani
authors.forename: Jingxi
authors.initials: J
authors.lastname: Lu
authors.forename: Tade
authors.initials: T
authors.lastname: Souaiaia
authors.forename: Yangho
authors.initials: Y
authors.lastname: Chen
authors.forename: Andrew
authors.initials: A
authors.lastname: Clark
authors.forename: Hee Jae
authors.initials: HJ
authors.lastname: Yoon
authors.forename: Lin
authors.initials: L
authors.lastname: Wan
authors.forename: Oleg V
authors.initials: OV
authors.lastname: Evgrafov
authors.forename: James A
authors.initials: JA
authors.lastname: Knowles
authors.forename: Ewa
authors.initials: E
authors.lastname: Deelman
authors.forename: Ting
authors.initials: T
authors.lastname: Chen
mesh_terms: D001483:Base Sequence; D015870:Gene Expression; D015894:Genome, Human; D006801:Humans; D012313:RNA; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D057188:Workflow
chemical_list: D012313:RNA