Plant bulk RNA-Seq workflow

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nControl miRNA FASTQ collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nTreated miRNA FASTQ collection"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Collection\nTreated mRNA FASTQ collection"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nPrecursor miRNA sequences"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Collection\nControl mRNA FASTQ collection"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nTranscriptome FASTA"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\nAnnotation GTF"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Dataset\nMature miRNA sequences"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["ℹ️ Input Dataset\nStar miRNA sequenes"];
  style 8 stroke:#2c3143,stroke-width:4px;
  9["FastQC"];
  0 -->|output| 9;
  10["Trim Galore!"];
  0 -->|output| 10;
  11["FastQC"];
  1 -->|output| 11;
  12["Trim Galore!"];
  1 -->|output| 12;
  13["FastQC"];
  2 -->|output| 13;
  14["FastQC"];
  4 -->|output| 14;
  15["Salmon quant"];
  6 -->|output| 15;
  2 -->|output| 15;
  5 -->|output| 15;
  16["Salmon quant"];
  6 -->|output| 16;
  4 -->|output| 16;
  5 -->|output| 16;
  17["FastQC"];
  10 -->|trimmed_reads_single| 17;
  18["MiRDeep2 Mapper"];
  10 -->|trimmed_reads_single| 18;
  19["Merge collections"];
  11 -->|text_file| 19;
  9 -->|text_file| 19;
  20["FastQC"];
  12 -->|trimmed_reads_single| 20;
  21["MiRDeep2 Mapper"];
  12 -->|trimmed_reads_single| 21;
  22["Merge collections"];
  13 -->|text_file| 22;
  14 -->|text_file| 22;
  23["DESeq2"];
  15 -->|output_gene_quant| 23;
  16 -->|output_gene_quant| 23;
  6 -->|output| 23;
  24["MiRDeep2 Quantifier"];
  7 -->|output| 24;
  3 -->|output| 24;
  18 -->|output_reads_collapsed| 24;
  8 -->|output| 24;
  25["MultiQC"];
  19 -->|output| 25;
  26["Merge collections"];
  20 -->|text_file| 26;
  17 -->|text_file| 26;
  27["MiRDeep2 Quantifier"];
  7 -->|output| 27;
  3 -->|output| 27;
  21 -->|output_reads_collapsed| 27;
  8 -->|output| 27;
  28["MultiQC"];
  22 -->|output| 28;
  29["Filter"];
  23 -->|deseq_out| 29;
  30["Cut"];
  24 -->|miRNAsExpressed| 30;
  31["MultiQC"];
  26 -->|output| 31;
  32["Cut"];
  27 -->|miRNAsExpressed| 32;
  33["Filter"];
  29 -->|out_file1| 33;
  34["Filter"];
  29 -->|out_file1| 34;
  35["DESeq2"];
  32 -->|out_file1| 35;
  30 -->|out_file1| 35;
  36["Cut"];
  34 -->|out_file1| 36;
  37["Filter"];
  35 -->|deseq_out| 37;
  38["Filter FASTA"];
  36 -->|out_file1| 38;
  5 -->|output| 38;
  39["Filter"];
  37 -->|out_file1| 39;
  40["Filter"];
  37 -->|out_file1| 40;
  41["Cut"];
  40 -->|out_file1| 41;
  42["Filter FASTA"];
  41 -->|out_file1| 42;
  8 -->|output| 42;
  43["Filter FASTA"];
  41 -->|out_file1| 43;
  7 -->|output| 43;
  44["Concatenate datasets"];
  43 -->|output| 44;
  42 -->|output| 44;
  45["TargetFinder"];
  38 -->|output| 45;
  44 -->|out_file1| 45;

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/mirna-target-finder/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