RNA Seq Reads To Counts

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nInput FASTQs collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nInput Reference gene BED"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["Infer Experiment"];
  5 -->|output_alignments| 10;
  1 -->|output| 10;
  11["Read Distribution"];
  5 -->|output_alignments| 11;
  1 -->|output| 11;
  12["Column Join"];
  6 -->|output_short| 12;
  13["MultiQC"];
  4 -->|text_file| 13;
  3 -->|report| 13;
  10 -->|output| 13;
  7 -->|metrics_file| 13;
  8 -->|output| 13;
  9 -->|outputtxt| 13;
  11 -->|output| 13;
  6 -->|output_summary| 13;
  5 -->|summary_file| 13;
  2["FastQC raw reads"];
  0 -->|output| 2;
  3["Cutadapt"];
  0 -->|output| 3;
  4["FastQC post QC"];
  3 -->|out1| 4;
  5["HISAT2"];
  3 -->|out1| 5;
  6["featureCounts"];
  5 -->|output_alignments| 6;
  7["MarkDuplicates"];
  5 -->|output_alignments| 7;
  8["Samtools idxstats"];
  5 -->|output_alignments| 8;
  9["Gene Body Coverage BAM"];
  5 -->|output_alignments| 9;
  1 -->|output| 9;

Inputs

Outputs

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

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/transcriptomics/tutorials/rna-seq-reads-to-counts/workflows/rna-seq-reads-to-counts.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