Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2
Version 1

Workflow Type: Galaxy

Workflow for 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. Finally, the clusters are manually annotated with the help of marker genes. In an alternative step, the fragment file can also be generated from a BAM file.

newer Version: Updated SnapATAC2 version from 2.5.3 to 2.6.4

SEEK ID: https://workflowhub.eu/workflows/1077?version=1

Inputs

ID	Name	Description	Type
Bam-file	Bam-file	n/a	File
Fragment_file	Fragment_file	n/a	File
genes	Keys for annotations of obs/cells or vars/genes	Comma-separated list of obs/cells and vars/genes	string
Replace_file	Replace_file	n/a	File
chromosome_sizes.tabular	chromosome_sizes.tabular	n/a	File
gene_annotation	gene_annotation	n/a	File

Steps

ID	Name	Description
6	pp.import_data	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
7	pp.make_fragment_file	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
8	pl.frag_size_distr	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.5.3+galaxy2
9	pl.frag_size_distr_log	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.5.3+galaxy2
10	metrics.tsse	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
11	pp.import_data-sorted_by_barcodes	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
12	pl.tsse	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.5.3+galaxy2
13	pp.filter_cells	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
14	pp.add_tile_matrix	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
15	pp.select_features	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
16	pp.scrublet	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
17	pp.filter_doublets	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
18	tl.spectral	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.5.3+galaxy2
19	tl.umap	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.5.3+galaxy2
20	pp.knn	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.5.3+galaxy2
21	tl.leiden	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.5.3+galaxy2
22	pl.umap	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.5.3+galaxy2
23	make_gene_matrix	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
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

Outputs

ID	Name	Description	Type
plot frag_size	plot frag_size	n/a	File
plot log frag_size	plot log frag_size	n/a	File
anndata tsse	anndata tsse	n/a	File
anndata	anndata	n/a	File
plot tsse	plot tsse	n/a	File
anndata filter cells	anndata filter cells	n/a	File
anndata tile matrix	anndata tile matrix	n/a	File
anndata select features	anndata select features	n/a	File
anndata scrublet	anndata scrublet	n/a	File
anndata filter doublets	anndata filter doublets	n/a	File
anndata spectral	anndata spectral	n/a	File
anndata umap	anndata umap	n/a	File
anndata knn	anndata knn	n/a	File
anndata_leiden_clustering	anndata_leiden_clustering	n/a	File
umap_leiden-clusters	umap_leiden-clusters	n/a	File
anndata gene matrix	anndata gene matrix	n/a	File
anndata filter genes	anndata filter genes	n/a	File
anndata normalize	anndata normalize	n/a	File
anndata log1p	anndata log1p	n/a	File
anndata_magic	anndata_magic	n/a	File
anndata_gene-matrix_leiden	anndata_gene-matrix_leiden	n/a	File
umap_marker-genes	umap_marker-genes	n/a	File
leiden annotation	leiden annotation	n/a	File
cell type annotation	cell type annotation	n/a	File
anndata_cell_type	anndata_cell_type	n/a	File
umap_cell-type	umap_cell-type	n/a	File