Sofware: eRNA--A graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing

Abstact: eRNA focuses on the common tools required for the mapping and quantification analysis of miRNA-seq and mRNA-seq data. The software package provides an additional choice for scientists who require a user-friendly computing environment and high-throughput capacity for large data analysis. eRNA is available for free download at https://sourceforge.net/projects/erna/?source=directory.

Advances in high-throughput sequencing (HTS) technologies have achieved the analysis of genome-wide RNA profiles with high accuracy and unprecedentedly deep coverage while costs continue to decrease. The Illumina HiSeq 2500 sequencing system is able to sequence 192 RNA samples (multiplexed 24 samples in a single lane) up to six billion paired-end reads in a run (http://support.illumina.com/). Due to its high capacity, RNA sequencing (RNA-seq) has become a necessary research approach for transcriptomic studies and integrated systems analyses.

As far, many bioinformatics tools have been developed to support the identification of known RNAs and analysis of RNA expression profiles. A common workflow for micro-RNA sequencing (miRNA-seq) analysis includes adapter removal, sequence alignment, and read counting. To complete this process, various tools have been developed,including DSAP , E-miR , miRanalyzer , miRDeep2 , MIReNA , miRExpress , miRNAkey , miRspring , mirTools , and SeqBuster. Unlike miRNA-seq, a popular workflow for mRNA sequencing (mRNA-seq) analysis includes genome mapping, transcript assembling, and differential expression analysis, each separately accomplished by a combination of standalone tools (namely a combination of Bowtie, SAMtools, TopHat, and Cufflinks) and R packages in R environments. Some open source analytic workbenches or software solutions have been developed to integrate these different third-party tools, such as ArrayExpressHTS , Chipster , ExpressionPlot, GENE-Counter, GenePattern (www.broadinstitute.org/cancer/software/genepattern/modules/RNA-seq), GeneProf , RNA-seq Toolkit (RST), RobiNA, and TCW.

eRNA can be operated in a user friendly running environment. eRNA's interface has a main cascade graphic user interface (GUI) where multiple button operations trigger three-cascade sub-windows. All of the operations for each module are accompanied by step-by-step guides, and all parameters required for data analysis can be set through the GUIs. eRNA is divided into several functional GUI-based modules, which can be flexibly used in any combination or separately operated based on the requirements for data analysis. The modules "Self-testing", "miRNA identification", "mRNA identification", and "Target screening" are presented as notebook pages in the main graphic interface (Figure 1). Due to the long duration of data analysis, a visualization bar is added to show the program running status, and at the same time a monitoring GUI is also activated to show the analytic status of each sample as well as the computer system load. eRNA also supports a refreshing run after the first-time setup for time saving. Users can easily revise any parameters in a certain step based on previous results, and the refreshing run will not change the results determined by previous steps in the eRNA's pipeline. If a computer lacks support for Perl-Gtk2, eRNA can be operated by command. Users can revise all variables in the parameters file "variables.txt" (It is always in the result directory set by users) in command-line mode, of which parameter setup, especially in the third-party tools integrated in eRNA, is more flexible.

Figure 1: GUIs of eRNA

Writing data: 2013.12.01, 2015.02.06