RNA CoMPASS, a web-based GUI distributed computational pipeline, provides all-in-one functionality including human transcriptome quantification and the typical endogenous RNA-Sequencing analysis along with the investigation of exogenous sequences. RNA CoMPASS is deployable on either a local cluster or a grid environment managed by PBS submission.
Features
- Discovery and visualization of exogenous sequences of non-host origin
* Aligns short RNA sequences against human, virus and bacterial genomes
* Searches unmapped sequences against human RNA and NT databases
* Visualizes taxonomic distribution of reads using MEGAN
* Assembles pools of exogenous reads into longer transcripts with ABySS
(Currently under development)
- Performs extensive endogenous RNA-Seq analysis for the host organism
* Calculates genomic feature abundance score at both gene and isoform level
* Detects differentially expressed genes and isoforms with support for edgeR
* Generates wiggle files for visualization and signal maps for peak detection
* Generates alignment report summarizing distribution of read mappings
Contributors
Guorong Xu (Developer of RNA CoMPASS)
Joseph Coco (Developer of PARSES)
Mike Strong (Ph.D. Student), School of Medicine, Tulane University
Dr. Erik Flemington's lab, School of Medicine, Tulane University
Dr. Christopher Taylor (Supervisor), School of Medicine, Louisiana State University
Publications
Differences in Gastric Carcinoma Microenvironment Stratify According to EBV Infection Intensity: Implications for Possible Immune Adjuvant Therapy. Strong MJ#, Xu G#, Coco J, Baribault C, Vinay DS, Lacey MR, Strong AL, Lehman TA, Seddon MB, Lin Z, Concha M, Baddoo M, Ferris M, Swan KF, Sullivan DE, Burow ME, Taylor CM, Flemington EK. PLoS Pathog. 2013 May.
Whole-genome sequencing of the akata and mutu epstein-barr virus strains. Lin Z, Wang X, Strong MJ, Concha M, Baddoo M, Xu G, Baribault C, Fewell C, Hulme W, Hedges D, Taylor CM, Flemington EK. J Virol. 2013 Jan.
Detection of murine leukemia virus in the Epstein-Barr virus-positive human B-cell line JY, using a computational RNA-Seq-based exogenous agent detection pipeline, PARSES. Lin Z, Puetter A, Coco J, Xu G, Strong MJ, Wang X, Fewell C, Baddoo M, Taylor CM, Flemington EK. J Virol. 2012 Mar.
Downloads
Getting Help
RNA CoMPASS is hosted by SourceForge.net. The project page is here. The source codes are available from the download page.
©copyright 2012-2013 UNO Computational Biology Group. Created by Guorong Xu 2012.
Data Flow of RNA CoMPASS
Release and Updates
RNA CoMPASS v1.1 release 2013-5-24
RNA CoMPASS v1.0 release 2012-3-11
