Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2 2.0
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Run on GalaxyWorkflow of Tutorial "Single-cell ATAC-seq standard processing with SnapATAC2". This workflow takes a fragment file as input and performs the standard steps of scATAC-seq analysis: filtering, dimension reduction, embedding and visualization of marker genes with SnapATAC2. In an alternative step, the fragment file can also be generated from a BAM file.
Associated Tutorial
This workflows is part of the tutorial Single-cell ATAC-seq standard processing with SnapATAC2, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
- Uses Galaxy Workflow Comments
Thanks to...
Workflow Author(s): Timon Schlegel
Tutorial Author(s): Timon Schlegel
Tutorial Contributor(s): Pavankumar Videm, Björn Grüning, Saskia Hiltemann, Timon Schlegel, Wendi Bacon, Martin Čech, Armin Dadras
Funder(s): ELIXIR Europe, de.NBI, University of Freiburg
Grants(s): EuroScienceGateway
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Bam-file | Bam-file | n/a |
|
| Fragment_file | Fragment_file | n/a |
|
| genes | Keys for annotations of obs/cells or vars/genes | Comma-separated list of obs/cells and vars/genes |
|
| Replace_file | Replace_file | n/a |
|
| chromosome_sizes.tabular | chromosome_sizes.tabular | n/a |
|
| gene_annotation | gene_annotation | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 6 | pp.import_data | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 7 | pp.make_fragment_file | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 8 | pl.frag_size_distr | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1 |
| 9 | pl.frag_size_distr_log | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1 |
| 10 | metrics.tsse | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 11 | pp.import_data-sorted_by_barcodes | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 12 | pl.tsse | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1 |
| 13 | pp.filter_cells | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 14 | pp.add_tile_matrix | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 15 | pp.select_features | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 16 | pp.scrublet | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 17 | pp.filter_doublets | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 18 | tl.spectral | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1 |
| 19 | tl.umap | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1 |
| 20 | pp.knn | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1 |
| 21 | tl.leiden | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1 |
| 22 | pl.umap | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1 |
| 23 | make_gene_matrix | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 24 | scanpy_filter_genes | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy3 |
| 25 | Normalize | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy3 |
| 26 | pp.log1p | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy3 |
| 27 | external.pp.magic | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy3 |
| 28 | Copy obsm | toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0 |
| 29 | umap_plot_with_scanpy | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy3 |
| 30 | Inspect observations | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 |
| 31 | Cut leiden from table | Cut1 |
| 32 | Replace leiden | toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2 |
| 33 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0 |
| 34 | Plot cell types | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy3 |
| 35 | Final Anndata general info | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| plot frag_size | plot frag_size | n/a |
|
| plot log frag_size | plot log frag_size | n/a |
|
| anndata tsse | anndata tsse | n/a |
|
| anndata | anndata | n/a |
|
| plot tsse | plot tsse | n/a |
|
| anndata filter cells | anndata filter cells | n/a |
|
| anndata tile matrix | anndata tile matrix | n/a |
|
| anndata select features | anndata select features | n/a |
|
| anndata scrublet | anndata scrublet | n/a |
|
| anndata filter doublets | anndata filter doublets | n/a |
|
| anndata spectral | anndata spectral | n/a |
|
| anndata umap | anndata umap | n/a |
|
| anndata knn | anndata knn | n/a |
|
| anndata_leiden_clustering | anndata_leiden_clustering | n/a |
|
| umap_leiden-clusters | umap_leiden-clusters | n/a |
|
| anndata gene matrix | anndata gene matrix | n/a |
|
| anndata filter genes | anndata filter genes | n/a |
|
| anndata normalize | anndata normalize | n/a |
|
| anndata log1p | anndata log1p | n/a |
|
| anndata_magic | anndata_magic | n/a |
|
| anndata_gene-matrix_leiden | anndata_gene-matrix_leiden | n/a |
|
| umap_marker-genes | umap_marker-genes | n/a |
|
| leiden annotation | leiden annotation | n/a |
|
| cell type annotation | cell type annotation | n/a |
|
| anndata_cell_type | anndata_cell_type | n/a |
|
| umap_cell-type | umap_cell-type | n/a |
|
| general | general | n/a |
|
Version History
master
Creators and Submitter
Views: 41 Downloads: 4 Runs: 0
Created: 2nd Jun 2025 at 10:58
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