Hi-C Analysis with Galaxy Tutorial Workflow

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nHiC_S2_1p_10min_lowU_R1.fastq.gz"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nHiC_S2_1p_10min_lowU_R2.fastq.gz"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\ndm3_genome.fasta"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nGM12878_25kb_cooler_coarsen.cool"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\ncorrected_contact_matrix_dm3_large.h5"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nH3K36me3.bw"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\nH3K27me3.bw"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Dataset\nH4K16ac.bw"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["ℹ️ Input Dataset\ndm3_genes.bed"];
  style 8 stroke:#2c3143,stroke-width:4px;
  9["Bowtie2"];
  0 -->|output| 9;
  10["Bowtie2"];
  1 -->|output| 10;
  11["hicFindRestSite"];
  2 -->|output| 11;
  12["hicInfo"];
  3 -->|output| 12;
  13["hicDetectLoops"];
  3 -->|output| 13;
  14["hicInfo"];
  4 -->|output| 14;
  15["hicPCA"];
  4 -->|output| 15;
  16["hicFindTADs"];
  4 -->|output| 16;
  17["hicBuildMatrix"];
  11 -->|restrictionSites| 17;
  9 -->|output| 17;
  10 -->|output| 17;
  18["hicPlotMatrix"];
  13 -->|output_loops| 18;
  3 -->|output| 18;
  19["hicPlotMatrix"];
  15 -->|pearson_outfile| 19;
  15 -->|pca1| 19;
  20["hicPlotMatrix"];
  15 -->|pearson_outfile| 20;
  15 -->|pca2| 20;
  21["pyGenomeTracks"];
  16 -->|domains| 21;
  4 -->|output| 21;
  16 -->|tad_score| 21;
  15 -->|pca1| 21;
  15 -->|pca2| 21;
  5 -->|output| 21;
  6 -->|output| 21;
  7 -->|output| 21;
  8 -->|output| 21;
  16 -->|domains| 21;
  22["hicCorrectMatrix"];
  17 -->|outFileName| 22;
  23["hicMergeMatrixBins"];
  17 -->|outFileName| 23;
  24["hicCorrectMatrix"];
  17 -->|outFileName| 24;
  25["hicPlotMatrix"];
  22 -->|outFileName| 25;
  26["hicPlotMatrix"];
  23 -->|outFileName| 26;

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/epigenetics/tutorials/hicexplorer/workflows/Hi-C_Analysis_with_Galaxy_Tutorial_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