RNA-RNA interactome data analysis - chira v1.4.3

transcriptomics-rna-interactome/rna-rna-interactome-data-analysis-chira

Author(s)

Version
1
Last updated
Dec 4, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
RNA
transcriptomics

Features
Tutorial
RNA-RNA interactome data analysis
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00247
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
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

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/chira_collapse/chira_collapse/1.4.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/chira_extract/chira_extract/1.4.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.4.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/chira_merge/chira_merge/1.4.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/chira_quantify/chira_quantify/1.4.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5 View in ToolShed

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 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