Department of Biological Sciences, USC, Los Angeles, CA 90089, USA.
Bioinformatics. 2011 Sep 15;27(18):2598-600. doi: 10.1093/bioinformatics/btr441. Epub 2011 Jul 27.
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.
http://genomics.isi.edu/rnaseq
wangying@xmu.edu.cn; knowles@med.usc.edu; deelman@isi.edu; tingchen@usc.edu
Supplementary data are available at Bioinformatics online.
我们开发了一种针对 Illumina 单端测序reads 的 RNA-Seq 分析工作流程，称为 RseqFlow。该工作流程包括一系列分析功能，如测序数据的质量控制、映射reads 的信号轨迹、表达水平的计算、差异表达基因的鉴定和编码 SNP 调用。该工作流程由 Pegasus 工作流管理系统形式化和管理，该系统将分析模块映射到可用的计算资源上，自动按适当的顺序执行步骤，并监督整个运行过程。RseqFlow 作为一个包含所有必要软件的虚拟机提供，消除了任何复杂的配置和安装步骤。
http://genomics.isi.edu/rnaseq
wangying@xmu.edu.cn；knowles@med.usc.edu；deelman@isi.edu；tingchen@usc.edu
补充数据可在 Bioinformatics 在线获得。
