CelSeq2: Single Batch (mm10)

single-cell-scrna-preprocessing/scrna-pp-celseq

Author(s)

Version
1
Last updated
Nov 18, 2022
License
None Specified, defaults to CC-BY-4.0
Tags
transcriptomics

Features
Tutorial
Pre-processing of Single-Cell RNA Data
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00209
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Collection\nBatch"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nBarcodes single-col"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nGTF file UCSC"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["UMI-tools extract"];
  1 -->|output| 3;
  0 -->|output| 3;
  4["Alignment Choose a Genome"];
  2 -->|output| 4;
  3 -->|out2| 4;
  5["Filter"];
  4 -->|mapped_reads| 5;
  6["featureCounts"];
  5 -->|out_file1| 6;
  2 -->|output| 6;
  7["UMI-tools count"];
  6 -->|output_bam| 7;

Inputs

Input Label
Input dataset collection Batch
Input dataset Barcodes (single-col)
Input dataset GTF file (UCSC)

Outputs

From Output Label
Input dataset collection Batch
Input dataset Barcodes (single-col)
Input dataset GTF file (UCSC)
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2 UMI-tools extract
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2 RNA STAR Alignment (Choose a Genome)
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2 featureCounts
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2 UMI-tools count

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2 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
1 327fd2b84 2022-11-12 17:14:25 Making a single cell topics

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-preprocessing/workflows/scrna_pp_celseq.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