Workflows

These workflows are associated with RNA-RNA interactome data analysis

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.

RNA-RNA interactome data analysis - chira v1.4.3

Last updated Dec 4, 2020

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License: None Specified, defaults to CC-BY-4.0
Tests: ✅ Results: Not yet automated

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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;

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