Generating a single cell matrix using Alevin

single-cell-scrna-case_alevin/generating-a-single-cell-matrix-using-alevin

Author(s)
Julia Jakiela, Wendi Bacon
version Version
2
last_modification Last updated
Jun 13, 2024
license License
CC-BY-4.0
galaxy-tags Tags

Features

Tutorial
hands_on Generating a single cell matrix using Alevin

Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00194
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
  0["ℹ️ Input Dataset\nGTF file"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nReference FASTA"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nRead 1 - containing cell barcode & UMI"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nRead 2 - containing transcript"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["GTF2GeneList"];
  0 -->|output| 4;
  5["Transcript-gene mapping"];
  1 -->|output| 5;
  0 -->|output| 5;
  773cb4ae-56c3-49c0-b582-ee69d620def3["Output\nfasta_output"];
  5 --> 773cb4ae-56c3-49c0-b582-ee69d620def3;
  style 773cb4ae-56c3-49c0-b582-ee69d620def3 stroke:#2c3143,stroke-width:4px;
  a30424b5-1ddc-4324-9ff6-dc5883adcce0["Output\nfeature_annotation"];
  5 --> a30424b5-1ddc-4324-9ff6-dc5883adcce0;
  style a30424b5-1ddc-4324-9ff6-dc5883adcce0 stroke:#2c3143,stroke-width:4px;
  6["Alevin Processed"];
  2 -->|output| 6;
  3 -->|output| 6;
  5 -->|fasta_output| 6;
  1 -->|output| 6;
  5 -->|feature_annotation| 6;
  a87beb55-1baf-458e-bd09-bb5ac6ea6e9a["Output\nraw_cb_frequency_txt"];
  6 --> a87beb55-1baf-458e-bd09-bb5ac6ea6e9a;
  style a87beb55-1baf-458e-bd09-bb5ac6ea6e9a stroke:#2c3143,stroke-width:4px;
  c9390a50-775c-4f0f-88e5-0984d570902c["Output\nsalmon_quant_log"];
  6 --> c9390a50-775c-4f0f-88e5-0984d570902c;
  style c9390a50-775c-4f0f-88e5-0984d570902c stroke:#2c3143,stroke-width:4px;
  2cebc438-ddc0-41e0-89ba-49b4bd3e2160["Output\nquants_mat_mtx"];
  6 --> 2cebc438-ddc0-41e0-89ba-49b4bd3e2160;
  style 2cebc438-ddc0-41e0-89ba-49b4bd3e2160 stroke:#2c3143,stroke-width:4px;
  89fa1aad-9ec6-4351-97d5-f05cac09e08e["Output\nquants_mat_cols_txt"];
  6 --> 89fa1aad-9ec6-4351-97d5-f05cac09e08e;
  style 89fa1aad-9ec6-4351-97d5-f05cac09e08e stroke:#2c3143,stroke-width:4px;
  3b3dda80-5d35-4c51-9ca0-90a2f909755f["Output\nquants_mat_rows_txt"];
  6 --> 3b3dda80-5d35-4c51-9ca0-90a2f909755f;
  style 3b3dda80-5d35-4c51-9ca0-90a2f909755f stroke:#2c3143,stroke-width:4px;
  7["Alevin - no processing"];
  2 -->|output| 7;
  3 -->|output| 7;
  5 -->|fasta_output| 7;
  1 -->|output| 7;
  5 -->|feature_annotation| 7;
  25d4d8f6-d166-4470-80fe-d0fdb0702371["Output\nquants_mat_rows_txt_1"];
  7 --> 25d4d8f6-d166-4470-80fe-d0fdb0702371;
  style 25d4d8f6-d166-4470-80fe-d0fdb0702371 stroke:#2c3143,stroke-width:4px;
  d9ed1457-792b-4eaf-a9fc-2407bcd90da7["Output\nquants_mat_mtx_1"];
  7 --> d9ed1457-792b-4eaf-a9fc-2407bcd90da7;
  style d9ed1457-792b-4eaf-a9fc-2407bcd90da7 stroke:#2c3143,stroke-width:4px;
  40df6aa8-3dfa-4946-bbc8-cacf4ca2a20e["Output\nquants_mat_cols_txt_1"];
  7 --> 40df6aa8-3dfa-4946-bbc8-cacf4ca2a20e;
  style 40df6aa8-3dfa-4946-bbc8-cacf4ca2a20e stroke:#2c3143,stroke-width:4px;
  8["Droplet rank plot - raw barcodes"];
  6 -->|raw_cb_frequency_txt| 8;
  9["Droplet rank plot - Alevin barcodes"];
  6 -->|quants_mat_mtx| 9;
  10["salmonKallistoMtxTo10x"];
  7 -->|quants_mat_rows_txt| 10;
  7 -->|quants_mat_cols_txt| 10;
  7 -->|quants_mat_mtx| 10;
  11["Join two Datasets"];
  10 -->|genes_out| 11;
  4 -->|feature_annotation| 11;
  12["Cut"];
  11 -->|out_file1| 12;
  13["DropletUtils Read10x"];
  10 -->|barcodes_out| 13;
  12 -->|out_file1| 13;
  10 -->|matrix_out| 13;
  14["DropletUtils emptyDrops"];
  13 -->|output_rds| 14;
  15["SCEasy Converter"];
  14 -->|output_rdata| 15;

Inputs

Input Label
Input dataset GTF file
Input dataset Reference FASTA
Input dataset Read 1 - containing cell barcode & UMI
Input dataset Read 2 - containing transcript

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0 GTF2GeneList Transcript-gene mapping
toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0 Alevin Alevin Processed
toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0 Alevin Alevin - no processing

Tools

Tool Links
Cut1
join1
toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x/0.0.1+galaxy6 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/sceasy_convert/sceasy_convert/0.0.7+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
  • Click on Workflow on the top menu bar of Galaxy. 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
2 927da941a 2024-03-22 08:26:16 add workflow tests
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-case_alevin/workflows/Generating-a-single-cell-matrix-using-Alevin.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