Generating a single cell matrix using Alevin 1.0
Visit source
Download RO-Crate
Run on GalaxyThis workflow generates a single cell matrix using Alevin.
Associated Tutorial
This workflows is part of the tutorial Generating a single cell matrix using Alevin, available in the GTN
Thanks to...
Workflow Author(s): Julia Jakiela, Wendi Bacon
Tutorial Author(s): Wendi Bacon, Jonathan Manning
Tutorial Contributor(s): Helena Rasche, Julia Jakiela, Pavankumar Videm, Björn Grüning, Marisa Loach, Wendi Bacon, Teresa Müller, Saskia Hiltemann, Mehmet Tekman, Jonathan Manning, Beatriz Serrano-Solano, David López
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| GTF file | GTF file | You can find the file containing the gene information for your species here: http://www.ensembl.org/info/data/ftp/index.html/ |
|
| Read 1 - containing cell barcode & UMI | Read 1 - containing cell barcode & UMI | This should be a fast file containing the shorter read - i.e. the cell barcode and the unique molecular identifier |
|
| Read 2 - containing transcript | Read 2 - containing transcript | This should be the read containing the transcript |
|
| Reference FASTA | Reference FASTA | You can find this file for your species here: http://www.ensembl.org/info/data/ftp/index.html/ |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | GTF2GeneList | toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0 |
| 5 | Transcript-gene mapping | toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0 |
| 6 | Alevin Processed | toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0 |
| 7 | Alevin - no processing | toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0 |
| 8 | Droplet rank plot - raw barcodes | toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2 |
| 9 | Droplet rank plot - Alevin barcodes | toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2 |
| 10 | salmonKallistoMtxTo10x | toolshed.g2.bx.psu.edu/repos/ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x/0.0.1+galaxy6 |
| 11 | Join two Datasets | join1 |
| 12 | Cut | Cut1 |
| 13 | DropletUtils Read10x | toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0 |
| 14 | DropletUtils emptyDrops | toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0 |
| 15 | SCEasy Converter | toolshed.g2.bx.psu.edu/repos/iuc/sceasy_convert/sceasy_convert/0.0.7+galaxy2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| fasta_output | fasta_output | n/a |
|
| feature_annotation | feature_annotation | n/a |
|
| raw_cb_frequency_txt | raw_cb_frequency_txt | n/a |
|
| salmon_quant_log | salmon_quant_log | n/a |
|
| quants_mat_mtx | quants_mat_mtx | n/a |
|
| quants_mat_cols_txt | quants_mat_cols_txt | n/a |
|
| quants_mat_rows_txt | quants_mat_rows_txt | n/a |
|
| quants_mat_rows_txt_1 | quants_mat_rows_txt_1 | n/a |
|
| quants_mat_mtx_1 | quants_mat_mtx_1 | n/a |
|
| quants_mat_cols_txt_1 | quants_mat_cols_txt_1 | n/a |
|
Version History
master
Creators and Submitter
Views: 1139 Downloads: 181 Runs: 0
Created: 2nd Jun 2025 at 10:57
AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
I'm a bot managed by @hexylena to upload workflows from the Galaxy Training Network to the WorkflowHub. If you have any issues with my behaviour please let her know by filing an issue.
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
