ATAC-seq GTM

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nbed file with genes"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nctcf peaks"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nATAC R2 read in fastq.gz format"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nATAC R1 read in fastq.gz format"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Filter"];
  1 -->|output| 4;
  5["FastQC"];
  2 -->|output| 5;
  6["ATAC remove nextera adapters with cutadapt"];
  3 -->|output| 6;
  2 -->|output| 6;
  7["FastQC"];
  3 -->|output| 7;
  8["bedtools Intersect intervals"];
  4 -->|out_file1| 8;
  0 -->|output| 8;
  9["FastQC"];
  6 -->|out2| 9;
  10["Bowtie2"];
  6 -->|out1| 10;
  6 -->|out2| 10;
  11["FastQC"];
  6 -->|out1| 11;
  12["Filter BAM ATAC"];
  10 -->|output| 12;
  13["MarkDuplicates"];
  12 -->|out_file1| 13;
  14["bedtools BAM to BED"];
  13 -->|outFile| 14;
  15["Paired-end histogram"];
  13 -->|outFile| 15;
  16["MACS2 callpeak"];
  14 -->|output| 16;
  17["Wig/BedGraph-to-bigWig"];
  16 -->|output_treat_pileup| 17;
  18["computeMatrix"];
  17 -->|out_file1| 18;
  0 -->|output| 18;
  19["pyGenomeTracks"];
  17 -->|out_file1| 19;
  16 -->|output_narrowpeaks| 19;
  0 -->|output| 19;
  1 -->|output| 19;
  20["computeMatrix"];
  17 -->|out_file1| 20;
  8 -->|output| 20;
  65159c9c-050b-4069-8704-8f66c0563a98["Output\ncomputeMatrix on input dataset(s): Matrix"];
  20 --> 65159c9c-050b-4069-8704-8f66c0563a98;
  style 65159c9c-050b-4069-8704-8f66c0563a98 stroke:#2c3143,stroke-width:4px;
  21["plotHeatmap"];
  18 -->|outFileName| 21;
  22["plotHeatmap"];
  20 -->|outFileName| 22;
  74a36643-b88f-4378-8f9c-c1b20ee2651e["Output\nplotHeatmap on input dataset(s): Image"];
  22 --> 74a36643-b88f-4378-8f9c-c1b20ee2651e;
  style 74a36643-b88f-4378-8f9c-c1b20ee2651e stroke:#2c3143,stroke-width:4px;

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/cut_and_run/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