Long non-coding RNAs (lncRNAs) annotation with FEELnc

genome-annotation-lncrna/main-workflow

Author(s)
Stéphanie Robin
version Version
1
last_modification Last updated
Sep 23, 2022
license License
GPL-3.0-or-later
galaxy-tags Tags
genome-annotation

Features

Tutorial
hands_on Long non-coding RNAs (lncRNAs) annotation with FEELnc

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00097
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
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;

Inputs

Input Label
Input dataset mapped_RNASeq.bam
Input dataset genome_annotation.gff3
Input dataset genome_assembly.fasta

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/feelnc/feelnc/0.2 FEELnc
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 Concatenate datasets

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/feelnc/feelnc/0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.6 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 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
1 8b7050722 2022-09-23 14:33:06 Add a new tutorial about lncRNAs annotation (with FEELnc) (#3623)

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