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

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Workflow Type: Galaxy

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, available in the GTN

Features

Thanks to...

Tutorial Author(s): Timon Schlegel

Tutorial Contributor(s): Pavankumar Videm, Björn Grüning

Workflow Author(s): Timon Schlegel

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1343?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
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
  • 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
general general n/a
  • File

Version History

2.0 (latest) Created 12th Aug 2024 at 14:06 by Helena Rasche

Added/updated 4 files


Open master 9401f7e

1.0 (earliest) Created 12th Jul 2024 at 14:25 by Helena Rasche

Added/updated 4 files


Frozen 1.0 9ea0066
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GTN Matrix
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SCANPY
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Activity

Views: 445   Downloads: 157

Created: 12th Jul 2024 at 14:25

Last updated: 12th Aug 2024 at 14:06

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