Generating a single cell matrix using Alevin

Run Workflow in Galaxy

• Galaxy Australia
• Galaxy Europe
• Galaxy France
• Galaxy Main
• Import to another server (≥23.0+ only!)

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;

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

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:

Version History

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