🐳 Galaxy Docker repository for guided RNA-Seq analysis
| Tool | Description | Reference |
|---|---|---|
| FastQC | A quality control tool for high throughput sequence data | - |
| MultiQC | Bioinformatics analysis result aggregator | - |
| Trim Galore! | Quality control tool for read trimming and filtering of NGS data | - |
| Trimmomatic | Quality control tool for read trimming and filtering of Illumina NGS data | Bolger et al. 2014 |
| Tool | Description | Reference |
|---|---|---|
| SortMeRNA | A tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and -genomic data | Kopylova et al. 2011 |
| RESeQC | Visualization of RNA-Seq data | Wang et al. 2012 |
| Tool | Description | Reference |
|---|---|---|
| Bowtie2 | Fast and sensitive read alignment | Langmead et al. 2012 |
| BWA | Software package for mapping low-divergent sequences against a large reference genome | Li and Durbin 2009, Li and Durbin 2010 |
| HISAT2 | Hierarchical indexing for spliced alignment of transcripts | Pertea et al. 2016 |
| segemehl | Short sequence read to reference genome mapper | Hoffmann et al. 2009 |
| STAR | Rapid spliced aligner for RNA-seq data | Dobin et al. 2013 |
| TopHat | Splice junction mapper for RNA-Seq reads. TopHat aligns RNA-Seq reads to mammalian-sized genomes using the short read aligner Bowtie, then analyzes the results to identify splice junctions between exons | Trapnell et al. 2009 |
| Tool | Description | Reference |
|---|---|---|
| ViennaRNA | A software library of tools for predicting and comparing RNA secondary structures | Lorenz et al. 2011 |
| Tool | Description | Reference |
|---|---|---|
| featureCounts | Genomic feature read count tool for summarising of genes, exons, and promoter counts | Liao et al. 2014 |
| htseq-count | Tool for counting reads in features | Anders et al. 2015 |
| Tool | Description | Reference |
|---|---|---|
| Cufflinks | Estimation of transcripts abundances, and tests for differential expression and regulation in RNA-Seq samples | Trapnell et al. 2012 |
| CummeRbund | Visualize Cufflinks RNA-Seq output | - |
| DESeq2 | Differential gene expression analysis based on the negative binomial distribution | Love et al. 2014 |
| DeXSeq | Differential exon usage, using RNA-seq exon counts between samples with different experimental designs | Anders et al. 2012 |
| Tool | Description | Reference |
|---|---|---|
| SAMtools | Utilities for manipulating alignments in the SAM format | Heng et al. 2009 |
| deepTools | A software library of tools for exploring high throughput sequencing data | Ramirez et al. 2014, Ramirez et al. 2016 |
To launch:
docker run -d -p 8080:80 destairdenbi/galaxy-guided-rna-seq:latest
To launch with a permanent storage of databases, histories, etc:
docker run -d -p 8080:80 -v ~/galaxy-guided-rna-seq_DB:/export destairdenbi/galaxy-guided-rna-seq:latest
To access:
http://localhost
docker run --net host -d -p 8080:80 destairdenbi/galaxy-guided-rna-seq:latest
For more details about this command line or specific usage, please consult the
README of the main Galaxy Docker image, on which the current image is based.
git clone --recursive https://github.com/destairdenbi/galaxy-guided-rna-seq.git
cd galaxy-guided-rna-seq
docker built -t destairdenbi/galaxy-guided-rna-seq:17.05 .
- Andrea Bagnacani
- Bérénice Batut
- Bjoern Gruening
- Steffen Lott
- Konstantin Riege
- Markus Wolfien
- 0.1: Initial release!
You can file an issue, or contact us here.
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.