Whole transcriptome analysis of Arabidopsis thaliana

Run Workflow in Galaxy

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• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Collection\nControl miRNA"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nBR treated miRNA"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nmiRNA_stem-loop_seq.fasta"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nmiRNA_DESeq2_results_complete_dataset"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nmature_miRNA_AT.fasta"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nstar_miRNA_seq.fasta"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\nmRNA_DESeq2_results_complete_dataset.tabular"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Dataset\ntranscriptome.fasta"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["ℹ️ Input Collection\nBR treated mRNA"];
  style 8 stroke:#2c3143,stroke-width:4px;
  9["ℹ️ Input Collection\nControl mRNA"];
  style 9 stroke:#2c3143,stroke-width:4px;
  10["ℹ️ Input Dataset\nannotation_AtRTD2.gtf"];
  style 10 stroke:#2c3143,stroke-width:4px;
  11["Falco"];
  0 -->|output| 11;
  12["Trim Galore!"];
  0 -->|output| 12;
  13["Falco"];
  1 -->|output| 13;
  14["Trim Galore!"];
  1 -->|output| 14;
  15["Filter"];
  3 -->|output| 15;
  16["Filter"];
  6 -->|output| 16;
  17["Falco"];
  8 -->|output| 17;
  18["Falco"];
  9 -->|output| 18;
  19["Salmon quant"];
  10 -->|output| 19;
  8 -->|output| 19;
  7 -->|output| 19;
  20["Salmon quant"];
  10 -->|output| 20;
  9 -->|output| 20;
  7 -->|output| 20;
  21["Falco"];
  12 -->|trimmed_reads_single| 21;
  22["MiRDeep2 Mapper"];
  12 -->|trimmed_reads_single| 22;
  23["Merge collections"];
  11 -->|text_file| 23;
  13 -->|text_file| 23;
  24["Falco"];
  14 -->|trimmed_reads_single| 24;
  25["MiRDeep2 Mapper"];
  14 -->|trimmed_reads_single| 25;
  26["Filter"];
  15 -->|out_file1| 26;
  27["Filter"];
  16 -->|out_file1| 27;
  28["Filter"];
  16 -->|out_file1| 28;
  29["Merge collections"];
  18 -->|text_file| 29;
  17 -->|text_file| 29;
  30["DESeq2"];
  19 -->|output_gene_quant| 30;
  20 -->|output_gene_quant| 30;
  10 -->|output| 30;
  fa5917e8-0ccd-4918-aa4f-6a5ce0ef59c2["Output\nDESeq2 results subsample mRNA"];
  30 --> fa5917e8-0ccd-4918-aa4f-6a5ce0ef59c2;
  style fa5917e8-0ccd-4918-aa4f-6a5ce0ef59c2 stroke:#2c3143,stroke-width:4px;
  31["MiRDeep2 Quantifier"];
  4 -->|output| 31;
  2 -->|output| 31;
  22 -->|output_reads_collapsed| 31;
  5 -->|output| 31;
  32["MultiQC"];
  23 -->|output| 32;
  33["Merge collections"];
  21 -->|text_file| 33;
  24 -->|text_file| 33;
  34["MiRDeep2 Quantifier"];
  4 -->|output| 34;
  2 -->|output| 34;
  25 -->|output_reads_collapsed| 34;
  5 -->|output| 34;
  35["Sort"];
  26 -->|out_file1| 35;
  36["Cut"];
  26 -->|out_file1| 36;
  37["Cut"];
  28 -->|out_file1| 37;
  38["MultiQC"];
  29 -->|output| 38;
  39["Cut"];
  31 -->|miRNAsExpressed| 39;
  40["MultiQC"];
  33 -->|output| 40;
  41["Cut"];
  34 -->|miRNAsExpressed| 41;
  42["Filter FASTA"];
  36 -->|out_file1| 42;
  4 -->|output| 42;
  43["Filter FASTA"];
  36 -->|out_file1| 43;
  5 -->|output| 43;
  44["Filter FASTA"];
  37 -->|out_file1| 44;
  7 -->|output| 44;
  45["DESeq2"];
  41 -->|out_file1| 45;
  39 -->|out_file1| 45;
  73bf0109-9ccd-4718-bea0-9f66a05882fb["Output\nDESeq2 results subsample miRNA"];
  45 --> 73bf0109-9ccd-4718-bea0-9f66a05882fb;
  style 73bf0109-9ccd-4718-bea0-9f66a05882fb stroke:#2c3143,stroke-width:4px;
  46["Concatenate datasets"];
  42 -->|output| 46;
  43 -->|output| 46;
  47["Filter"];
  45 -->|deseq_out| 47;
  48["TargetFinder"];
  44 -->|output| 48;
  46 -->|out_file1| 48;
  35422953-279c-488a-a82c-cfbf4951aed5["Output\nTargetFinder output"];
  48 --> 35422953-279c-488a-a82c-cfbf4951aed5;
  style 35422953-279c-488a-a82c-cfbf4951aed5 stroke:#2c3143,stroke-width:4px;

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

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. 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