scATAC-seq FASTQ to Count Matrix
single-cell-scatac-preprocessing-tenx/scatac-seq-fastq-to-count-matrix
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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
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
- 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
- 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:
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