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

Download RO-Crate Run on Galaxy
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

Version History

Version 1 (earliest) Created 17th Jul 2024 at 16:56 by Timon Schlegel

Initial commit


Open master c8d3e5f
help Creators and Submitter
Creator
  • Timon Schlegel
Submitter
Tools
SCANPY
anndata
License
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Activity

Views: 4207   Downloads: 427   Runs: 3

Created: 17th Jul 2024 at 16:56

Last updated: 2nd Aug 2024 at 19:08

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Total size: 959 KB
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