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Welcome to the RNA Galaxy workbench 2.0 {:.no_toc}
The RNA Galaxy workbench is a comprehensive set of analysis tools and consolidated workflows. The workbench is based on the Galaxy framework, which guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses independent of command-line knowledge.
The current implementation comprises more than 700 bioinformatics tools dedicated to different research areas of RNA biology, including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-Seq analysis, and RNA target prediction. Out of these 700 tools about 100 tools were integrated into galaxy by us and the remaining are from the galaxy community efforts.
The workbench is developed by the RNA Bioinformatics Center (RBC) {:target="_blank"}. This center is one of the eight service units of the German Network for Bioinformatics Infrastructure (de.NBI) {:target="_blank"}, running the German ELIXIR Node {:target="_blank"}.
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If you find this resource useful, please cite The RNA workbench 2.0: next generation RNA data analysis {:target="_blank"}.
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TOC
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Are you new to Galaxy, or returning after a long time, and looking for help to get started? Take [a guided tour]({{ page.website }}/tours/core.galaxy_ui){:target="_blank"} through Galaxy's user interface.
We are passionate about training. So we are working in close collaboration with the Galaxy Training Network (GTN) {:target="_blank"} to develop training materials of data analyses based on Galaxy {% cite batut2017community %}. These materials hosted on the GTN GitHub repository are available online at https://training.galaxyproject.org {:target="_blank"}.
Want to learn more about RNA analyses? Take one of our guided tour or check out the following hands-on tutorials. We developed several tutorials and the remaining are from the GTN community (marked with
Lesson
Slides
Hands-on
Input dataset
Workflows
Galaxy tour
Galaxy History
Introduction to Transcriptomics
RNA-seq counts to genes
RNA-seq genes to pathways
RNA-Seq reads to counts
Analyse unaligned ncRNAs
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CLIP-Seq data analysis from pre-processing to motif detection
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De novo transcriptome reconstruction with RNA-Seq
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Differential abundance testing of small RNAs
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Network analysis with Heinz
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PAR-CLIP analysis
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Reference-based RNA-Seq data analysis
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RNA family model construction
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RNA-RNA interactome data analysis
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RNA-seq counts to genes
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RNA-seq genes to pathways
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RNA-Seq reads to counts
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Scan for C/D-box sequences with segmentation-fold
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Small Non-coding RNA Clustering using BlockClust
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Visualization of RNA-Seq results with CummeRbund
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Visualization of RNA-Seq results with Volcano Plot
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Visualization of RNA-Seq results with heatmap2
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ViennaRNA Introduction
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In this section we list all tools that have been integrated in the RNA workbench. The list is likely to grow as soon as further tools and workflows are contributed. To ease readability, we divided them into categories.
RNA structure prediction and analysis
Tool
Description
Reference
{% include tool.html id="antaRNA" %}
Possibility of inverse RNA structure folding and a specification of a GC value constraint
Kleinkauf et al. 2015 {:target="_blank"}
{% include tool.html id="CoFold" %}
A thermodynamics-based RNA secondary structure folding algorithm
Proctor and Meyer, 2015 {:target="_blank"}
{% include tool.html id="Kinwalker" %}
Algorithm for cotranscriptional folding of RNAs to obtain the min. free energy structure
Geis et al. 2008 {:target="_blank"}
{% include tool.html id="MEA" %}
Prediction of maximum expected accuracy RNA secondary structures
Amman et al. 2013 {:target="_blank"}
{% include tool.html id="RNAshapes" %}
Structures to a tree-like domain of shapes, retaining adjacency and nesting of structural features
Janssen and Giergerich, 2014 {:target="_blank"}
{% include tool.html id="RNAz" %}
Predicts structurally conserved and therm. stable RNA secondary structures in mult. seq. alignments
Washietl et al. 2005 {:target="_blank"}
{% include tool.html id="segmentation-fold" %}
An application that predicts RNA 2D-structure with an extended version of the Zuker algorithm
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ViennaRNA
A tool compilation for prediction and comparison of RNA secondary structures
Lorenz et al. 2011 {:target="_blank"}
{: .table.table-striped .tooltable}
Tool
Description
Reference
{% include tool.html id="Compalignp" %}
An RNA counterpart of the protein specific "Benchmark Alignment Database"
Wilm et al. 2006 {:target="_blank"}
{% include tool.html id="LocARNA" %}
A tool for multiple alignment of RNA molecules
Will et al. 2012 {:target="_blank"}
{% include tool.html id="MAFFT" %}
A multiple sequence alignment program for unix-like operating systems
Katoh and Standley, 2016 {:target="_blank"}
{% include tool.html id="RNAlien" %}
A tool for RNA family model construction
Eggenhofer et al. 2016 {:target="_blank"}
{% include tool.html id="CMV" %}
RNA family model visualisation
Eggenhofer et al. 2018 {:target="_blank"}
{: .table.table-striped .tooltable}
Tool
Description
Reference
{% include tool.html id="ARAGORN" %}
A tool to identify tRNA and tmRNA genes
Laslett and Canback, 2004 {:target="_blank"}
{% include tool.html id="Fusion Matcher (FuMa)" %}
A tool that reports identical fusion genes based on gene-name annotations
Hoogstrate et al. 2016 {:target="_blank"}
{% include tool.html id="GotohScan" %}
A search tool that finds shorter sequences in large database sequences
Hertel et al. 2009 {:target="_blank"}
{% include tool.html id="INFERNAL" %}
A tool searching DNA sequence databases for RNA structure and sequence similarities
Nawrocki et al. 2015 {:target="_blank"}
{% include tool.html id="RNABOB" %}
A tool for fast pattern searching for RNA secondary structures
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{% include tool.html id="RNAcode" %}
Predicts protein coding regions in a a set of homologous nucleotide sequences
Washietl et al. 2011 {:target="_blank"}
{% include tool.html id="tRNAscan" %}
Searches for tRNA genes in genomic sequences
Lowe and Eddy, 1997 {:target="_blank"}
{% include tool.html id="RCAS" %}
A generic reporting tool for the functional analysis of transcriptome-wide regions of interest detected by high-throughput experiments
Uyar et al. {:target="_blank"}
{: .table.table-striped .tooltable}
Tool
Description
Reference
{% include tool.html id="AREsite2" %}
A database for AU-/GU-/U-rich elements in human and model organisms
Fallmann et al. 2016 {:target="_blank"}
{% include tool.html id="DoRiNA" %}
A database of RNA interactions in post-transcriptional regulation
Blin et al. 2014 {:target="_blank"}
{% include tool.html id="PARalyzer" %}
An algorithm to generate a map of interacting RNA-binding proteins and their targets
Corcoran et al. 2011 {:target="_blank"}
{% include tool.html id="Piranha" %}
A peak-caller for CLIP- and RIP-seq data
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{: .table.table-striped .tooltable}
Tool
Description
Reference
{% include tool.html id="chira_collapse" label="C" %}{% include tool.html id="chira_map" label="h" %}{% include tool.html id="chira_merge" label="i" %}{% include tool.html id="chira_quantify" label="R" %}{% include tool.html id="chira_extract" label="A" %}
A set of tools to analyze RNA interactome/structurome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH etc
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{: .table.table-striped .tooltable}
Tool
Description
Reference
{% include tool.html id="TargetFinder" %}
A tool to predict small RNA binding sites on target transcripts from a sequence database
-
{: .table.table-striped .tooltable}
Tool
Description
Reference
{% include tool.html id="FastQC" %}
A quality control tool for high throughput sequence data
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{% include tool.html id="TrimGalore" label="Trim Galore!" %}
Automatic quality and adapter trimming as well as quality control
-
{: .table.table-striped .tooltable}
Tool
Description
Reference
{% include tool.html id="BlockClust" %}
Small non-coding RNA clustering from deep sequencing read profiles
Videm et al. 2014 {:target="_blank"}
{% include tool.html id="FlaiMapper" %}
A tool for computational annotation of small ncRNA-derived fragments using RNA-seq data
Hoogstrate et al. 2015 {:target="_blank"}
{% include tool.html id="MiRDeep2" %}
Discovers microRNA genes by analyzing sequenced RNAs
Friedländer et al. 2008 {:target="_blank"}
{% include tool.html id="NASTIseq" %}
A method that incorporates the inherent variable efficiency of generating perfectly strand-specific libraries
Li et al. 2013 {:target="_blank"}
{% include tool.html id="PIPmiR" %}
An algorithm to identify novel plant miRNA genes from a combination of deep sequencing data and genomic features
Breakfield et al. 2011 {:target="_blank"}
{% include tool.html id="SortMeRNA" %}
A tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and -genomic data
Kopylova et al. 2011 {:target="_blank"}
{: .table.table-striped .tooltable}
Tool
Description
Reference
{% include tool.html id="hisat2" %}
Hierarchical indexing for spliced alignment of transcripts
Pertea et al. 2016 {:target="_blank"}
{% include tool.html id="RNA STAR" %}
Rapid spliced aligner for RNA-seq data
Dobin et al. 2013 {:target="_blank"}
{% include tool.html id="STAR-fusion" %}
Fast fusion gene finder
Haas et al. 2017 {:target="_blank"}
{% include tool.html id="bowtie2" %}
Fast and sensitive read alignment
Langmead et al. 2012 {:target="_blank"}
{% include tool.html id="BWA" %}
Software package for mapping low-divergent sequences against a large reference genome
Li and Durbin 2009 {:target="_blank"}, Li and Durbin 2010 {:target="_blank"}
{: .table.table-striped .tooltable}
Tool
Description
Reference
{% include tool.html id="Trinity" %}
De novo transcript sequence reconstruction from RNA-Seq
Haas et al. 2013 {:target="_blank"}
{: .table.table-striped .tooltable}
Tool
Description
Reference
{% include tool.html id="featureCounts" %}
Ultrafast and accurate read summarization program
Liao et al. 2014 {:target="_blank"}
{% include tool.html id="htseq-count" %}
Tool for counting reads in features
Anders et al. 2015 {:target="_blank"}
{% include tool.html id="Sailfish" %}
Rapid Alignment-free Quantification of Isoform Abundance
Patro et al. 2014 {:target="_blank"}
{% include tool.html id="Salmon" %}
Fast, accurate and bias-aware transcript quantification
Patro et al. 2017 {:target="_blank"}
{: .table.table-striped .tooltable}
Differential expression analysis
Tool
Description
Reference
{% include tool.html id="DESeq2" %}
Differential gene expression analysis based on the negative binomial distribution
Love et al. 2014 {:target="_blank"}
{: .table.table-striped .tooltable}
Tool
Description
Reference
RiboTaper
An analysis pipeline for Ribo-Seq experiments, exploiting the triplet periodicity of ribosomal footprints to call translated regions
Calviello et al. 2016 {:target="_blank"}
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