RNA-RNA interactome data analysis - chira v1.4.3
transcriptomics-rna-interactome/rna-rna-interactome-data-analysis-chira
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flowchart TD 0["ℹ️ Input Dataset\nreads_fastq"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nreference1_fasta"]; style 1 stroke:#2c3143,stroke-width:4px; 2["ℹ️ Input Dataset\nreference2_fasta"]; style 2 stroke:#2c3143,stroke-width:4px; 3["ℹ️ Input Dataset\nannotation_gtf"]; style 3 stroke:#2c3143,stroke-width:4px; 4["ℹ️ Input Dataset\ngenome_fasta"]; style 4 stroke:#2c3143,stroke-width:4px; 5["FastQC"]; 0 -->|output| 5; 6["Cutadapt"]; 0 -->|output| 6; 7["FastQC"]; 6 -->|out1| 7; 8["ChiRA collapse"]; 6 -->|out1| 8; 9["ChiRA map"]; 8 -->|out| 9; 1 -->|output| 9; 2 -->|output| 9; 10["ChiRA merge"]; 9 -->|mapped_bed| 10; 3 -->|output| 10; 1 -->|output| 10; 2 -->|output| 10; 11["ChiRA qauntify"]; 10 -->|merged_bed| 11; 10 -->|segments_bed| 11; 12["ChiRA extract"]; 4 -->|output| 12; 3 -->|output| 12; 11 -->|loci| 12; 1 -->|output| 12; 2 -->|output| 12; 7182226d-b48a-4ce1-882e-6bb41091a5d4["Output\ninteractions"]; 12 --> 7182226d-b48a-4ce1-882e-6bb41091a5d4; style 7182226d-b48a-4ce1-882e-6bb41091a5d4 stroke:#2c3143,stroke-width:4px; 011f4c89-d15a-4877-9d49-0146773ce781["Output\nchimeric_reads"]; 12 --> 011f4c89-d15a-4877-9d49-0146773ce781; style 011f4c89-d15a-4877-9d49-0146773ce781 stroke:#2c3143,stroke-width:4px; 13["Query Tabular"]; 12 -->|chimeras| 13; f1315db2-11d1-4dee-9014-eafa1fc0f82f["Output\ndb"]; 13 --> f1315db2-11d1-4dee-9014-eafa1fc0f82f; style f1315db2-11d1-4dee-9014-eafa1fc0f82f stroke:#2c3143,stroke-width:4px;
Inputs
Input | Label |
---|---|
Input dataset | reads_fastq |
Input dataset | reference1_fasta |
Input dataset | reference2_fasta |
Input dataset | annotation_gtf |
Input dataset | genome_fasta |
Outputs
From | Output | Label |
---|---|---|
Input dataset | reads_fastq | |
Input dataset | reference1_fasta | |
Input dataset | reference2_fasta | |
Input dataset | annotation_gtf | |
Input dataset | genome_fasta | |
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 | FastQC | |
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5 | Cutadapt | |
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 | FastQC | |
toolshed.g2.bx.psu.edu/repos/iuc/chira_collapse/chira_collapse/1.4.3+galaxy0 | ChiRA collapse | |
toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.4.3+galaxy0 | ChiRA map | |
toolshed.g2.bx.psu.edu/repos/iuc/chira_merge/chira_merge/1.4.3+galaxy0 | ChiRA merge | |
toolshed.g2.bx.psu.edu/repos/iuc/chira_quantify/chira_quantify/1.4.3+galaxy0 | ChiRA qauntify | |
toolshed.g2.bx.psu.edu/repos/iuc/chira_extract/chira_extract/1.4.3+galaxy0 | ChiRA extract | |
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 | Query Tabular |
Tools
To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.
Importing into Galaxy
Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!Hands-on: Importing a workflow
- Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
- Click on galaxy-upload Import at the top-right of the screen
- Provide your workflow
- Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
- Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
- Click the Import workflow button
Below is a short video demonstrating how to import a workflow from GitHub using this procedure:
Video: Importing a workflow from URL
Version History
Version | Commit | Time | Comments |
---|---|---|---|
2 | 1dde32698 | 2020-12-04 22:33:21 | update rna-rna interactome workflow and add workflow test |
1 | 922058fc6 | 2020-12-04 22:30:57 | update rna-rna interactome workflow and add workflow test |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-interactome/workflows/rna-rna-interactome-data-analysis-chira.ga -O workflow.ga workflow-to-tools -w workflow.ga -o tools.yaml shed-tools install -g GALAXY -a API_KEY -t tools.yaml workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows