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:  [email protected]; [email protected] …

Metadata

publication

Bioinformatics 27 (18), 2598-2600, 2011

year

2011

publication date

2011/9/15

authors

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

link

https://academic.oup.com/bioinformatics/article-abstract/27/18/2598/181908

resource_link

https://academic.oup.com/bioinformatics/article/27/18/2598/181908

journal

Bioinformatics

volume

27

issue

18

pages

2598-2600

publisher

Oxford University Press