RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

Recent rapid advances in next generation RNA sequencing (RNA-Seq)-based provide researchers with unprecedentedly large data sets and open new perspectives in transcriptomics. Furthermore, RNA-Seq-based transcript profiling can be applied to non-model and newly discovered organisms because it does not require a predefined measuring platform (like e.g. microarrays). However, these novel technologies pose new challenges: the raw data need to be rigorously quality checked and filtered prior to analysis, and proper statistical methods have to be applied to extract biologically relevant information. Given the sheer volume of data, this is no trivial task and requires a combination of considerable technical resources along with bioinformatics expertise. To aid the individual researcher, we have developed RobiNA as an integrated solution that consolidates all steps of RNA-Seq-based differential gene-expression analysis in one user-friendly cross-platform application featuring a rich graphical user interface. RobiNA accepts raw FastQ files, SAM/BAM alignment files and counts tables as input. It supports quality checking, flexible filtering and statistical analysis of differential gene expression based on state-of-the art biostatistical methods developed in the R/Bioconductor projects. In-line help and a step-by-step manual guide users through the analysis. Installer packages for Mac OS X, Windows and Linux are available under the LGPL licence from http://mapman.gabipd.org/web/guest/robin.

[1]  Mark D. Robinson,et al.  Differential Gene Expression in the Siphonophore Nanomia bijuga (Cnidaria) Assessed with Multiple Next-Generation Sequencing Workflows , 2011, PloS one.

[2]  Y. Benjamini,et al.  Summarizing and correcting the GC content bias in high-throughput sequencing , 2012, Nucleic acids research.

[3]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[4]  Dan Zhao,et al.  Upconversion emission from Yb3+ and Tm3+ codoped NaYF4 thin film prepared by thermal evaporation. , 2011, Journal of nanoscience and nanotechnology.

[5]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[6]  Dan Zhao,et al.  Ultraviolet upconversion fluorescence of Er3+ in Yb3+/Er3+-codoped Gd2O3 nanotubes. , 2011, Journal of nanoscience and nanotechnology.

[7]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[8]  Deming Liu,et al.  Synthesis and characterization of upconverting NaYF4:Er3+, Yb3+ nanocrystals via thermal decomposition of stearate precursor. , 2011, Journal of nanoscience and nanotechnology.

[9]  Matthew D. Young,et al.  From RNA-seq reads to differential expression results , 2010, Genome Biology.

[10]  Sandrine Dudoit,et al.  Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments , 2010, BMC Bioinformatics.

[11]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[12]  Daniel J. Blankenberg,et al.  Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists , 2010, Current protocols in molecular biology.

[13]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[14]  J. Mesirov,et al.  GenePattern 2.0 , 2006, Nature Genetics.

[15]  Joshua A Udall,et al.  Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata) , 2011, BMC Genomics.

[16]  Dan Zhao,et al.  Synthesis of monodisperse NaYF4:Yb, Tm@SiO2 nanoparticles with intense ultraviolet upconversion luminescence. , 2011, Journal of nanoscience and nanotechnology.

[17]  Mark Stitt,et al.  A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. , 2009, Plant, cell & environment.

[18]  Thomas J. Hardcastle,et al.  baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data , 2010, BMC Bioinformatics.

[19]  K. Hansen,et al.  Biases in Illumina transcriptome sequencing caused by random hexamer priming , 2010, Nucleic acids research.

[20]  Jun-Xia Zheng,et al.  [Study on the extraction technology of total flavonoids from Selaginella uncinata]. , 2011, Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials.

[21]  C. Su,et al.  De novo assembly of expressed transcripts and global analysis of the Phalaenopsis aphrodite transcriptome. , 2011, Plant & cell physiology.

[22]  B. Langmead,et al.  Cloud-scale RNA-sequencing differential expression analysis with Myrna , 2010, Genome Biology.

[23]  Daniel J. Blankenberg,et al.  Galaxy: a platform for interactive large-scale genome analysis. , 2005, Genome research.

[24]  Alyssa C. Frazee,et al.  ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets , 2011, BMC Bioinformatics.

[25]  Andreas Prlic,et al.  Sequence analysis , 2003 .

[26]  Dan Zhao,et al.  Synthesis and upconversion luminescence of NaYF4:Yb, Tm/TiO2 core/shell nanoparticles with controllable shell thickness. , 2011, Journal of nanoscience and nanotechnology.

[27]  Guorong Xu,et al.  SAMMate: a GUI tool for processing short read alignments in SAM/BAM format , 2011, Source Code for Biology and Medicine.

[28]  Joachim Selbig,et al.  Robin: An Intuitive Wizard Application for R-Based Expression Microarray Quality Assessment and Analysis1[W][OA] , 2010, Plant Physiology.

[29]  Sandrine Dudoit,et al.  GC-Content Normalization for RNA-Seq Data , 2011, BMC Bioinformatics.

[30]  Peng Jin,et al.  Effect of 1-methylcyclopropene on chilling injury and quality of peach fruit during cold storage. , 2011, Journal of food science.

[31]  Sandrine Dudoit,et al.  Polygenic and directional regulatory evolution across pathways in Saccharomyces , 2010, Proceedings of the National Academy of Sciences.

[32]  Chih-Kuan Chen,et al.  Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses , 2011, Biotechnology for biofuels.

[33]  Li Yang,et al.  Conservation of an RNA regulatory map between Drosophila and mammals. , 2011, Genome research.

[34]  Heng Li,et al.  A survey of sequence alignment algorithms for next-generation sequencing , 2010, Briefings Bioinform..

[35]  Wei Zheng,et al.  Bias detection and correction in RNA-Sequencing data , 2011, BMC Bioinformatics.

[36]  Ying Cheng,et al.  The European Nucleotide Archive , 2010, Nucleic Acids Res..