scATAC-seq Count Matrix Filtering

single-cell-scatac-preprocessing-tenx/scatac-seq-count-matrix-filtering

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:W00192
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\nscATAC-seq Anndata"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["scATAC-seq Preprocessing"];
  0 -->|output| 1;
  2["scATAC-seq Preprocessing"];
  1 -->|anndata_out| 2;
  3["scATAC-seq Preprocessing"];
  2 -->|anndata_out| 3;
  4["Scanpy plot"];
  3 -->|anndata_out| 4;
  5["scATAC-seq Preprocessing"];
  3 -->|anndata_out| 5;
  6["scATAC-seq Preprocessing"];
  3 -->|anndata_out| 6;
  7["scATAC-seq Preprocessing"];
  3 -->|anndata_out| 7;
  8["scATAC-seq Preprocessing"];
  3 -->|anndata_out| 8;
  9["scATAC-seq Preprocessing"];
  8 -->|anndata_out| 9;
  10["scATAC-seq Preprocessing"];
  9 -->|anndata_out| 10;
  11["scATAC-seq Preprocessing"];
  10 -->|anndata_out| 11;
  019f2426-d144-4143-a7f2-60e51385623e["Output\nFiltered Anndata"];
  11 --> 019f2426-d144-4143-a7f2-60e51385623e;
  style 019f2426-d144-4143-a7f2-60e51385623e stroke:#2c3143,stroke-width:4px;
  12["Inspect AnnData"];
  11 -->|anndata_out| 12;
  c16d5f08-eb75-4332-bfbe-701af27395b4["Output\nAnndata info"];
  12 --> c16d5f08-eb75-4332-bfbe-701af27395b4;
  style c16d5f08-eb75-4332-bfbe-701af27395b4 stroke:#2c3143,stroke-width:4px;
  13["Scanpy plot"];
  11 -->|anndata_out| 13;
  fc369121-d4a3-4309-bf6a-7780767f52f6["Output\nout_png"];
  13 --> fc369121-d4a3-4309-bf6a-7780767f52f6;
  style fc369121-d4a3-4309-bf6a-7780767f52f6 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset scATAC-seq Anndata

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/episcanpy_preprocess/episcanpy_preprocess/0.3.2+galaxy1 scATAC-seq Preprocessing
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy1 Inspect AnnData
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2 Scanpy plot

Tools

Tool Links
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/episcanpy_preprocess/episcanpy_preprocess/0.3.2+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2 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
2 cdc14914d 2025-10-15 13:47:18 update the second workflow of filtering
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-Count-Matrix-Filtering.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