Infinium Human Methylation BeadChip

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nR01C02_Red.idat"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nR02C02_Red.idat"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nR05C02_Red.idat"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nR06C02_Red.idat"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nR01C02_Green.idat"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nR02C02_Green.idat"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\nR05C02_Green.idat"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Dataset\nR06C02_Green.idat"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["ℹ️ Input Dataset\nphenotype Table txt file"];
  style 8 stroke:#2c3143,stroke-width:4px;
  9["ℹ️ Input Dataset\nUCSC Main on Human"];
  style 9 stroke:#2c3143,stroke-width:4px;
  10["Infinium Human Methylation BeadChip"];
  4 -->|output| 10;
  5 -->|output| 10;
  6 -->|output| 10;
  7 -->|output| 10;
  0 -->|output| 10;
  1 -->|output| 10;
  2 -->|output| 10;
  3 -->|output| 10;
  8 -->|output| 10;
  9 -->|output| 10;
  2ac7dd5d-ed74-4d58-b1cb-be7dcca9154a["Output\nSNPInfo Table"];
  10 --> 2ac7dd5d-ed74-4d58-b1cb-be7dcca9154a;
  style 2ac7dd5d-ed74-4d58-b1cb-be7dcca9154a stroke:#2c3143,stroke-width:4px;
  d1732a98-1861-4612-bdaa-f68861c22f56["Output\nDifferentially Methylated Regions"];
  10 --> d1732a98-1861-4612-bdaa-f68861c22f56;
  style d1732a98-1861-4612-bdaa-f68861c22f56 stroke:#2c3143,stroke-width:4px;
  9aa8b4a9-611e-4a39-864f-400f17866a9e["Output\nDifferentially Methylated Positions"];
  10 --> 9aa8b4a9-611e-4a39-864f-400f17866a9e;
  style 9aa8b4a9-611e-4a39-864f-400f17866a9e stroke:#2c3143,stroke-width:4px;
  14ddb6f7-637e-4193-bfb5-80aeae4fab64["Output\nQuality Control Report"];
  10 --> 14ddb6f7-637e-4193-bfb5-80aeae4fab64;
  style 14ddb6f7-637e-4193-bfb5-80aeae4fab64 stroke:#2c3143,stroke-width:4px;
  c8c37ff8-716d-4c23-a84f-7cebcb4b6c9d["Output\nQuality Control Plot"];
  10 --> c8c37ff8-716d-4c23-a84f-7cebcb4b6c9d;
  style c8c37ff8-716d-4c23-a84f-7cebcb4b6c9d stroke:#2c3143,stroke-width:4px;
  11["ChIPpeakAnno annoPeaks"];
  10 -->|dmp| 11;
  bedf4346-da4d-4e1a-bf3c-a7d20f3ec3c5["Output\nTable of Annotated Peaks"];
  11 --> bedf4346-da4d-4e1a-bf3c-a7d20f3ec3c5;
  style bedf4346-da4d-4e1a-bf3c-a7d20f3ec3c5 stroke:#2c3143,stroke-width:4px;
  12["Cut"];
  11 -->|tab| 12;
  0b54dfe5-f84a-4288-b631-ae4dc2384a17["Output\nCut on Table of Annotated Peaks"];
  12 --> 0b54dfe5-f84a-4288-b631-ae4dc2384a17;
  style 0b54dfe5-f84a-4288-b631-ae4dc2384a17 stroke:#2c3143,stroke-width:4px;
  13["Remove beginning"];
  12 -->|out_file1| 13;
  8f65cf82-7427-4273-ba0b-a6673ee1ff2d["Output\nRemove beginning on the cut output"];
  13 --> 8f65cf82-7427-4273-ba0b-a6673ee1ff2d;
  style 8f65cf82-7427-4273-ba0b-a6673ee1ff2d stroke:#2c3143,stroke-width:4px;
  14["Cluster Profiler Bitr"];
  13 -->|out_file1| 14;
  7989f80a-3e79-4d2f-bbe4-e4d641eebd6a["Output\nTable of Translated Gene ID's"];
  14 --> 7989f80a-3e79-4d2f-bbe4-e4d641eebd6a;
  style 7989f80a-3e79-4d2f-bbe4-e4d641eebd6a stroke:#2c3143,stroke-width:4px;
  15["Cluster Profiler GO"];
  14 -->|translation| 15;
  ff6c7018-b821-4ade-9931-fa99aeb0a86c["Output\nGO Enrichment Analysis of a Gene Set"];
  15 --> ff6c7018-b821-4ade-9931-fa99aeb0a86c;
  style ff6c7018-b821-4ade-9931-fa99aeb0a86c stroke:#2c3143,stroke-width:4px;
  03b88399-095b-4bd5-9693-528c60338407["Output\nGO Enrichment Analysis Visualization"];
  15 --> 03b88399-095b-4bd5-9693-528c60338407;
  style 03b88399-095b-4bd5-9693-528c60338407 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

• 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/epigenetics/tutorials/ewas-suite/workflows/Infinium-Human-Methylation-BeadChip.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