scATAC-seq FASTQ to Count Matrix

single-cell-scatac-preprocessing-tenx/scatac-seq-fastq-to-count-matrix

Author(s)
Pavankumar Videm
Version
2
Last updated
Oct 16, 2025
License
CC-BY-4.0
Tags
name:single-cell

Features
Tutorial
Pre-processing of 10X Single-Cell ATAC-seq Datasets
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00193
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nBarcodes FASTQ R2"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nForward reads FASTQ R1"];
  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"];
  0 -->|output| 3;
  1 -->|output| 3;
  2 -->|output| 3;
  4["Falco"];
  3 -->|read1_out| 4;
  ee430f86-5aa2-4fbf-a7bc-8deb4aeb8c0f["Output\nFalco on R1"];
  4 --> ee430f86-5aa2-4fbf-a7bc-8deb4aeb8c0f;
  style ee430f86-5aa2-4fbf-a7bc-8deb4aeb8c0f stroke:#2c3143,stroke-width:4px;
  5["Map with BWA-MEM"];
  3 -->|read1_out| 5;
  3 -->|read2_out| 5;
  6["Falco"];
  3 -->|read2_out| 6;
  aa7c6e89-2fac-4b38-943a-4717bc678b19["Output\nFalco on R2"];
  6 --> aa7c6e89-2fac-4b38-943a-4717bc678b19;
  style aa7c6e89-2fac-4b38-943a-4717bc678b19 stroke:#2c3143,stroke-width:4px;
  7["Sinto fragments"];
  5 -->|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;
  adcce063-b4d3-4d8e-9d1e-5bb15247ac11["Output\nAnndata object"];
  11 --> adcce063-b4d3-4d8e-9d1e-5bb15247ac11;
  style adcce063-b4d3-4d8e-9d1e-5bb15247ac11 stroke:#2c3143,stroke-width:4px;
  12["Inspect AnnData"];
  11 -->|anndata_out| 12;
  13["Inspect AnnData"];
  11 -->|anndata_out| 13;
  14["Inspect AnnData"];
  11 -->|anndata_out| 14;
  420096ff-010d-46cd-abd8-5b34dd54c364["Output\nAnndata info"];
  14 --> 420096ff-010d-46cd-abd8-5b34dd54c364;
  style 420096ff-010d-46cd-abd8-5b34dd54c364 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Barcodes FASTQ (R2)
Input dataset Forward reads FASTQ (R1)
Input dataset Reverse reads FASTQ (R3)

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/1.2.4+galaxy0 Falco
toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/1.2.4+galaxy0 Falco
toolshed.g2.bx.psu.edu/repos/iuc/episcanpy_build_matrix/episcanpy_build_matrix/0.3.2+galaxy1 Build count matrix
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy1 Inspect AnnData

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.5+galaxy2
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/episcanpy_build_matrix/episcanpy_build_matrix/0.3.2+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/1.2.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/sinto_barcode/sinto_barcode/0.10.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/sinto_fragments/sinto_fragments/0.10.1+galaxy0 View in ToolShed

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

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands On: Importing a workflow
  1. Click on 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 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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
3 4811c9bc7 2025-10-15 13:42:54 add tests for the 1st workflow
2 e2833c265 2025-10-15 07:44:34 Fix a param in scATAC-seq preprocessing tutorial and update the tools
1 094d1948a 2023-04-24 12:23:27 Add workflow tests

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