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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.
The key features include,
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
The software is available for download at:
The key features include,
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
The software is available for download at:
