scATAC-seq FASTQ to Count Matrix

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

Author(s)
Pavankumar Videm
Version
1
Last updated
Apr 24, 2023
License
CC-BY-4.0
Tags

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\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;

Inputs

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

Outputs

From Output Label

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy2 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/macs2/macs2_callpeak/2.2.7.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/sinto_barcode/sinto_barcode/0.9.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/sinto_fragments/sinto_fragments/0.9.0+galaxy1 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
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