Long non-coding RNAs (lncRNAs) annotation with FEELnc

Run Workflow in Galaxy

• Galaxy Main
• Galaxy France
• Galaxy Australia
• Galaxy Europe
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nmapped_RNASeq.bam"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\ngenome_annotation.gff3"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\ngenome_assembly.fasta"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["StringTie"];
  1 -->|output| 3;
  0 -->|output| 3;
  4["gffread"];
  1 -->|output| 4;
  5["FEELnc"];
  3 -->|output_gtf| 5;
  2 -->|output| 5;
  4 -->|output_gtf| 5;
  4055b259-173c-492d-86a4-5e662b663421["Output\nmRNAs"];
  5 --> 4055b259-173c-492d-86a4-5e662b663421;
  style 4055b259-173c-492d-86a4-5e662b663421 stroke:#2c3143,stroke-width:4px;
  abc029ba-b7ba-4586-88b4-5e5d758c2f39["Output\nlncRNAs"];
  5 --> abc029ba-b7ba-4586-88b4-5e5d758c2f39;
  style abc029ba-b7ba-4586-88b4-5e5d758c2f39 stroke:#2c3143,stroke-width:4px;
  93ff3464-d1bb-4059-86af-3e703da3e542["Output\nClassifier output"];
  5 --> 93ff3464-d1bb-4059-86af-3e703da3e542;
  style 93ff3464-d1bb-4059-86af-3e703da3e542 stroke:#2c3143,stroke-width:4px;
  6["Concatenate datasets"];
  4 -->|output_gtf| 6;
  5 -->|candidate_lncRNA| 6;
  7b91b6a4-ef67-4359-9c93-eabcc021b0fc["Output\nfinal_annotation"];
  6 --> 7b91b6a4-ef67-4359-9c93-eabcc021b0fc;
  style 7b91b6a4-ef67-4359-9c93-eabcc021b0fc stroke:#2c3143,stroke-width:4px;

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

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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/lncrna/workflows/main_workflow.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