RseqFlow: workflows for RNA-Seq data analysis

被引：20

作者：

Wang, Ying ^{[1
,2
]}

Mehta, Gaurang ^{[3
]}

Mayani, Rajiv ^{[3
]}

Lu, Jingxi ^{[1
]}

Souaiaia, Tade ^{[1
]}

Chen, Yangho ^{[1
]}

Clark, Andrew ^{[4
]}

Yoon, Hee Jae ^{[4
]}

Wan, Lin ^{[1
]}

Evgrafov, Oleg V. ^{[4
]}

Knowles, James A. ^{[4
]}

Deelman, Ewa ^{[3
]}

Chen, Ting ^{[1
]}

机构：

[1] USC, Dept Biol Sci, Los Angeles, CA 90089 USA

[2] Xiamen Univ, Dept Automat, Xiamen, Peoples R China

[3] USC Informat Sci Inst, Marina Del Rey, CA 90292 USA

[4] USC Keck Sch Med, Dept Psychiat, Los Angeles, CA 90033 USA

来源：

BIOINFORMATICS | 2011年 / 27卷 / 18期

关键词：

EXPRESSION; ALIGNMENT;

D O I：

10.1093/bioinformatics/btr441

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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: http://bioinformatics.oxfordjournals.org/cgi/content/full/btr441/DC1 are available at Bioinformatics online.

引用

页码：2598 / 2600

页数：3

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