Abstract
Small RNA-Seq is a common means to interrogate the small RNA’ome or the full spectrum of small RNAs (<200 nucleotide length) of a biological system. A pivotal problem in NGS based small RNA analysis is identifying and quantifying the small RNA’ome constituent components. For example, small RNAs in the circulatory system (circulating RNAs) are potential disease biomarkers and their function is being actively investigated. Most existing NGS data analysis tools focus on the microRNA component and a few other small RNA types like piRNA, snRNA and snoRNA. A comprehensive platform is needed to interrogate the full small RNA’ome, a prerequisite for down-stream data analysis. We present COMPSRA, a comprehensive modular stand-alone platform for identifying and quantifying small RNAs from small RNA sequencing data. COMPSRA contains prebuilt customizable standard RNA databases and sequence processing tools to enable turnkey basic small RNA analysis. We evaluated COMPSRA against comparable existing tools on small RNA sequencing data set from serum samples of 12 healthy human controls, and COMPSRA identified a greater diversity and abundance of small RNA molecules. COMPSRA is modular, stand-alone and integrates multiple customizable RNA databases and sequence processing tool and is distributed under the GNU General Public License free to non-commercial registered users at https://github.com/cougarlj/COMPSRA.
Highlights
Small RNA sequencing (RNA-seq) technology was developed successfully based on special isolation methods and the RNA-seq technique, which facilitates the investigation of a comprehensive profile of small RNAs1,2
SRNAnalyzer is a comprehensive and customizable pipeline for the small RNA-seq data centred on microRNA profiling10. sRNAtoolbox is a web-based small RNA research toolkit[11] and SeqCluster has started to focus on non-miRNAs by comparing the sequence similarity[12]
Some efforts have begun to characterize the full spectrum of small RNAs of a biological system, such as Oasis[2], miRMaster and exceRpt[13,14,15]
Summary
Small RNA sequencing (RNA-seq) technology was developed successfully based on special isolation methods and the RNA-seq technique, which facilitates the investigation of a comprehensive profile of small RNAs1,2. To profile intracellular and extracellular small RNA’omes through the small RNA-seq data, we built a comprehensive platform COMPSRA to identify and quantify diverse RNA molecule types, including miRNA, piRNA, snRNA, snoRNA, tRNA, circRNA and the fragmental microbial RNA.
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