Name
Abstract | ||
|---|---|---|
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. |
Year | DOI | Venue |
|---|---|---|
2011 | 10.1093/bioinformatics/btr441 | BIOINFORMATICS |
Keywords | Field | DocType |
rna,virtual machine,data analysis,gene expression,workflow,quality control,analytic function,workflow management system | Genome,Data mining,RNA,RNA-Seq,Computer science,Genome human,Bioinformatics | Journal |
Volume | Issue | ISSN |
27 | 18 | 1367-4803 |
Citations | PageRank | References |
8 | 0.72 | 10 |
Authors | ||
13 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Ying Wang | 1 | 8 | 1.73 |
| Gaurang Mehta | 2 | 2355 | 168.62 |
| Rajiv Mayani | 3 | 197 | 10.84 |
| Jingxi Lu | 4 | 8 | 0.72 |
| Tade Souaiaia | 5 | 47 | 3.31 |
| Yangho Chen | 6 | 45 | 2.62 |
| Andrew P. Clark | 7 | 23 | 1.58 |
| Hee Jae Yoon | 8 | 8 | 0.72 |
| Lin Wan | 9 | 31 | 4.11 |
| Oleg V Evgrafov | 10 | 8 | 1.06 |
| James A. Knowles | 11 | 26 | 2.33 |
| Ewa Deelman | 12 | 5948 | 420.48 |
| Ting Chen | 13 | 2154 | 268.96 |