Workflows

These workflows are associated with Hi-C analysis of Drosophila melanogaster cells using HiCExplorer

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.

Galaxy Workflow Galaxy Hi C

Last updated Jan 23, 2020

Launch in Tutorial Mode
License: None Specified, defaults to CC-BY-4.0
Tests: ❌ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy France Galaxy Australia Galaxy Main Galaxy Europe Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\nR1.fastq"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nR2.fastq"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nH3K27me3.bw"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nH3K36me3.bw"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nH4K16ac.bw"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\ndm3_genes.bed"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["Map with BWA-MEM"];
  0 -->|output| 6;
  7["Map with BWA-MEM"];
  1 -->|output| 7;
  8["hicBuildMatrix"];
  7 -->|output| 8;
  6 -->|output| 8;
  9["hicMergeMatrixBins"];
  8 -->|outFileName| 9;
  10["hicCorrectMatrix"];
  8 -->|outFileName| 10;
  11["hicCorrectMatrix"];
  8 -->|outFileName| 11;
  12["hicPlotMatrix"];
  9 -->|outFileName| 12;
  13["hicPlotMatrix"];
  11 -->|outFileName| 13;
  14["hicFindTADs"];
  11 -->|outFileName| 14;
  15["hicPCA"];
  14 -->|matrix_output| 15;
  16["hicPlotTADs"];
  14 -->|domains| 16;
  11 -->|outFileName| 16;
  14 -->|tad_score| 16;
  15 -->|pca1| 16;
  15 -->|pca2| 16;
  3 -->|output| 16;
  2 -->|output| 16;
  4 -->|output| 16;
  5 -->|output| 16;

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 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