scATAC-seq FASTQ to Count Matrix

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nForward reads FASTQ R1"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nBarcodes FASTQ R2"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nReverse reads FASTQ R3"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Sinto barcode"];
  1 -->|output| 3;
  0 -->|output| 3;
  2 -->|output| 3;
  4["FastQC"];
  3 -->|read1_out| 4;
  5["FastQC"];
  3 -->|read2_out| 5;
  6["Map with BWA-MEM"];
  3 -->|read1_out| 6;
  3 -->|read2_out| 6;
  7["Sinto fragments"];
  6 -->|bam_output| 7;
  8["bedtools SortBED"];
  7 -->|fragments| 8;
  9["MACS2 callpeak"];
  8 -->|output| 9;
  10["Unique"];
  9 -->|output_narrowpeaks| 10;
  11["Build count matrix"];
  8 -->|output| 11;
  10 -->|outfile| 11;
  12["Inspect AnnData"];
  11 -->|anndata_out| 12;
  13["Inspect AnnData"];
  11 -->|anndata_out| 13;
  14["Inspect AnnData"];
  11 -->|anndata_out| 14;
  15["Inspect AnnData"];
  11 -->|anndata_out| 15;

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/single-cell/tutorials/scatac-preprocessing-tenx/workflows/scATAC-seq-FASTQ-to-Count-Matrix.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