LOCKED | Generating a single cell matrix using Alevin

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nRead 1 - containing cell barcode & UMI"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nRead 2 - containing transcript"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nReference FASTA"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nGTF file"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Transcript-gene mapping"];
  2 -->|output| 4;
  3 -->|output| 4;
  a30424b5-1ddc-4324-9ff6-dc5883adcce0["Output\nfeature_annotation"];
  4 --> a30424b5-1ddc-4324-9ff6-dc5883adcce0;
  style a30424b5-1ddc-4324-9ff6-dc5883adcce0 stroke:#2c3143,stroke-width:4px;
  773cb4ae-56c3-49c0-b582-ee69d620def3["Output\nfasta_output"];
  4 --> 773cb4ae-56c3-49c0-b582-ee69d620def3;
  style 773cb4ae-56c3-49c0-b582-ee69d620def3 stroke:#2c3143,stroke-width:4px;
  5["Gene Information Extraction"];
  3 -->|output| 5;
  b0a930ed-e61e-4f81-ac71-33454156535d["Output\nfasta_output2"];
  5 --> b0a930ed-e61e-4f81-ac71-33454156535d;
  style b0a930ed-e61e-4f81-ac71-33454156535d stroke:#2c3143,stroke-width:4px;
  2d37017a-4de8-4bfb-b55d-bd68e84dbca9["Output\nGene_Information"];
  5 --> 2d37017a-4de8-4bfb-b55d-bd68e84dbca9;
  style 2d37017a-4de8-4bfb-b55d-bd68e84dbca9 stroke:#2c3143,stroke-width:4px;
  6["Alevin - no processing"];
  0 -->|output| 6;
  1 -->|output| 6;
  4 -->|fasta_output| 6;
  4 -->|feature_annotation| 6;
  d9ed1457-792b-4eaf-a9fc-2407bcd90da7["Output\nquants_mat_mtx_1"];
  6 --> 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"];
  6 --> 40df6aa8-3dfa-4946-bbc8-cacf4ca2a20e;
  style 40df6aa8-3dfa-4946-bbc8-cacf4ca2a20e stroke:#2c3143,stroke-width:4px;
  25d4d8f6-d166-4470-80fe-d0fdb0702371["Output\nquants_mat_rows_txt_1"];
  6 --> 25d4d8f6-d166-4470-80fe-d0fdb0702371;
  style 25d4d8f6-d166-4470-80fe-d0fdb0702371 stroke:#2c3143,stroke-width:4px;
  50a32d87-f9a6-4725-b9d6-8f120be54f12["Output\nraw_cb_frequency_txt"];
  6 --> 50a32d87-f9a6-4725-b9d6-8f120be54f12;
  style 50a32d87-f9a6-4725-b9d6-8f120be54f12 stroke:#2c3143,stroke-width:4px;
  0250f882-c681-408d-9b85-ee2f0db9f943["Output\nsalmon_quant_log"];
  6 --> 0250f882-c681-408d-9b85-ee2f0db9f943;
  style 0250f882-c681-408d-9b85-ee2f0db9f943 stroke:#2c3143,stroke-width:4px;
  7["salmonKallistoMtxTo10x"];
  6 -->|quants_mat_rows_txt| 7;
  6 -->|quants_mat_cols_txt| 7;
  6 -->|quants_mat_mtx| 7;
  a5933f5d-7132-4778-b071-4402cc7149c5["Output\nbarcodes_out"];
  7 --> a5933f5d-7132-4778-b071-4402cc7149c5;
  style a5933f5d-7132-4778-b071-4402cc7149c5 stroke:#2c3143,stroke-width:4px;
  701ae85b-e70a-4600-a61c-060c604e490f["Output\nmatrix_out"];
  7 --> 701ae85b-e70a-4600-a61c-060c604e490f;
  style 701ae85b-e70a-4600-a61c-060c604e490f stroke:#2c3143,stroke-width:4px;
  7e1c350b-4ca8-43b8-b9e8-73c0b157bd70["Output\ngenes_out"];
  7 --> 7e1c350b-4ca8-43b8-b9e8-73c0b157bd70;
  style 7e1c350b-4ca8-43b8-b9e8-73c0b157bd70 stroke:#2c3143,stroke-width:4px;
  8["Droplet rank plot - raw barcodes"];
  6 -->|raw_cb_frequency_txt| 8;
  f8f35d85-c947-406e-a815-16d7d9b5fce1["Output\nplot_file-raw"];
  8 --> f8f35d85-c947-406e-a815-16d7d9b5fce1;
  style f8f35d85-c947-406e-a815-16d7d9b5fce1 stroke:#2c3143,stroke-width:4px;
  9["Join two Datasets"];
  7 -->|genes_out| 9;
  5 -->|feature_annotation| 9;
  84810b7f-eaef-4157-a952-1917bddab9f2["Output\nout_file1"];
  9 --> 84810b7f-eaef-4157-a952-1917bddab9f2;
  style 84810b7f-eaef-4157-a952-1917bddab9f2 stroke:#2c3143,stroke-width:4px;
  10["Cut"];
  9 -->|out_file1| 10;
  beb4d205-31a1-4d69-8c33-c787b3400d15["Output\nAnnotated_Gene_Table"];
  10 --> beb4d205-31a1-4d69-8c33-c787b3400d15;
  style beb4d205-31a1-4d69-8c33-c787b3400d15 stroke:#2c3143,stroke-width:4px;
  11["DropletUtils Read10x"];
  7 -->|barcodes_out| 11;
  10 -->|out_file1| 11;
  7 -->|matrix_out| 11;
  81418e51-8964-4648-aa00-4fdf3694ee29["Output\noutput_rds"];
  11 --> 81418e51-8964-4648-aa00-4fdf3694ee29;
  style 81418e51-8964-4648-aa00-4fdf3694ee29 stroke:#2c3143,stroke-width:4px;
  12["DropletUtils emptyDrops"];
  11 -->|output_rds| 12;
  d50c0da5-3028-493e-b63e-762f3c15d233["Output\noutput_rdata"];
  12 --> d50c0da5-3028-493e-b63e-762f3c15d233;
  style d50c0da5-3028-493e-b63e-762f3c15d233 stroke:#2c3143,stroke-width:4px;
  13["SCEasy Converter"];
  12 -->|output_rdata| 13;
  e3f0a5c6-9791-45f6-a8ce-7780bcc2db4a["Output\noutput_anndata"];
  13 --> e3f0a5c6-9791-45f6-a8ce-7780bcc2db4a;
  style e3f0a5c6-9791-45f6-a8ce-7780bcc2db4a stroke:#2c3143,stroke-width:4px;
  14["Inspect AnnData"];
  13 -->|output_anndata| 14;
  e5ee7a2f-55f4-4a01-83e5-31c0c388c281["Output\nvar"];
  14 --> e5ee7a2f-55f4-4a01-83e5-31c0c388c281;
  style e5ee7a2f-55f4-4a01-83e5-31c0c388c281 stroke:#2c3143,stroke-width:4px;
  15["Manipulate AnnData"];
  13 -->|output_anndata| 15;
  ca3447c7-2076-41a3-8e9b-0c2d7367386c["Output\nanndata"];
  15 --> ca3447c7-2076-41a3-8e9b-0c2d7367386c;
  style ca3447c7-2076-41a3-8e9b-0c2d7367386c stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

Tools

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

1. Click on galaxy-workflows-activity 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 galaxy-upload 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:

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