Preprocessing of 10X scRNA-seq data

single-cell-scrna-preprocessing-tenx/scrna-seq-preprocessing-tenx

Author(s)
Wendi Bacon, Pavankumar Videm, Mehmet Tekman, Hans-Rudolf Hotz, Daniel Blankenberg
Version
1
Last updated
May 19, 2023
License
CC-BY-4.0
Tags
single-cell
transcriptomics

Features
Tutorial
Pre-processing of 10X Single-Cell RNA Datasets
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00210
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\nHomo_sapiens.GRCh37.75.gtf"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nsubset_pbmc_1k_v3_S1_L001_R1_001.fastq.gz"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nsubset_pbmc_1k_v3_S1_L002_R1_001.fastq.gz"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nsubset_pbmc_1k_v3_S1_L002_R2_001.fastq.gz"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nsubset_pbmc_1k_v3_S1_L001_R2_001.fastq.gz"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\n3M-february-2018.txt.gz"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["RNA STARSolo"];
  0 -->|output| 6;
  1 -->|output| 6;
  2 -->|output| 6;
  3 -->|output| 6;
  4 -->|output| 6;
  5 -->|output| 6;
  7["DropletUtils"];
  6 -->|output_matrix| 7;
  6 -->|output_barcodes| 7;
  6 -->|output_genes| 7;
  8["DropletUtils"];
  6 -->|output_matrix| 8;
  6 -->|output_barcodes| 8;
  6 -->|output_genes| 8;
  9["DropletUtils"];
  6 -->|output_matrix| 9;
  6 -->|output_barcodes| 9;
  6 -->|output_genes| 9;

Inputs

Input Label
Input dataset Homo_sapiens.GRCh37.75.gtf
Input dataset subset_pbmc_1k_v3_S1_L001_R1_001.fastq.gz
Input dataset subset_pbmc_1k_v3_S1_L002_R1_001.fastq.gz
Input dataset subset_pbmc_1k_v3_S1_L002_R2_001.fastq.gz
Input dataset subset_pbmc_1k_v3_S1_L001_R2_001.fastq.gz
Input dataset 3M-february-2018.txt.gz

Outputs

From Output Label

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.10b+galaxy3 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
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on 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 a72ffa886 2023-05-18 19:07:53 add author ids
2 3dead543d 2023-05-18 19:02:57 Update workflow authors
1 5d8104ecc 2023-05-18 14:13:37 Update 10x scRNA preprocessing tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-preprocessing-tenx/workflows/scRNA-seq-Preprocessing-TenX.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