Workflow 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 [Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2](https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html), available in the [GTN](https://training.galaxyproject.org) ## Features * Includes [Galaxy Workflow Tests](https://training.galaxyproject.org/training-material/faqs/gtn/workflow_run_test.html) * Includes a [Galaxy Workflow Report](https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_report_view.html) * Uses [Galaxy Workflow Comments](https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_comments.html) ## Thanks to... **Tutorial Author(s)**: [Timon Schlegel](https://training.galaxyproject.org/training-material/hall-of-fame/timonschlegel/) **Tutorial Contributor(s)**: [Pavankumar Videm](https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/), [Björn Grüning](https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/) **Workflow Author(s)**: Timon Schlegel [](https://training.galaxyproject.org/training-material/)