ATAC-seq GTM

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nInput Paired End Collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nctcf peaks"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nbed file with genes"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ATAC remove nextera adapters with cutadapt"];
  0 -->|output| 3;
  d197ec94-1dec-41f4-b70f-7b350a07bdf7["Output\nreport"];
  3 --> d197ec94-1dec-41f4-b70f-7b350a07bdf7;
  style d197ec94-1dec-41f4-b70f-7b350a07bdf7 stroke:#2c3143,stroke-width:4px;
  4["Flatten collection"];
  0 -->|output| 4;
  5["Filter"];
  1 -->|output| 5;
  6["Bowtie2"];
  3 -->|out_pairs| 6;
  7["Flatten collection"];
  3 -->|out_pairs| 7;
  8["FastQC"];
  4 -->|output| 8;
  9["bedtools Intersect intervals"];
  5 -->|out_file1| 9;
  2 -->|output| 9;
  10["Filter BAM ATAC"];
  6 -->|output| 10;
  11["FastQC"];
  7 -->|output| 11;
  12["MarkDuplicates"];
  10 -->|out_file1| 12;
  13["Paired-end histogram"];
  12 -->|outFile| 13;
  14["bedtools BAM to BED"];
  12 -->|outFile| 14;
  15["MACS2 callpeak"];
  14 -->|output| 15;
  16["Wig/BedGraph-to-bigWig"];
  15 -->|output_treat_pileup| 16;
  17["pyGenomeTracks"];
  16 -->|out_file1| 17;
  15 -->|output_narrowpeaks| 17;
  2 -->|output| 17;
  1 -->|output| 17;
  18["computeMatrix"];
  16 -->|out_file1| 18;
  2 -->|output| 18;
  19["computeMatrix"];
  16 -->|out_file1| 19;
  9 -->|output| 19;
  78114e87-4bae-456d-b32b-3e0eed141052["Output\ncomputeMatrix on input dataset(s): Matrix"];
  19 --> 78114e87-4bae-456d-b32b-3e0eed141052;
  style 78114e87-4bae-456d-b32b-3e0eed141052 stroke:#2c3143,stroke-width:4px;
  20["plotHeatmap"];
  18 -->|outFileName| 20;
  21["plotHeatmap"];
  19 -->|outFileName| 21;
  67a173a4-2d79-43e7-b3fc-c250022a5c0a["Output\nplotHeatmap on input dataset(s): Image"];
  21 --> 67a173a4-2d79-43e7-b3fc-c250022a5c0a;
  style 67a173a4-2d79-43e7-b3fc-c250022a5c0a 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/epigenetics/tutorials/atac-seq/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