Multisample Batch Correction with SnapATAC2 and Harmony
Version 1

Download RO-Crate

Run on Galaxy

Workflow Type: Galaxy

This Workflow takes a dataset collection of single-cell ATAC-seq fragments and performs:

preprocessing
filtering
concatenation
dimension reduction
batch correction (with Harmony and optionally Scanorama and MNC-correct)
leiden clustering

new SnapATAC2 version: from 2.5.3 to 2.6.4

SEEK ID: https://workflowhub.eu/workflows/1078?version=1

Inputs

ID	Name	Description	Type
Input MultiSample Collection	Input MultiSample Collection	n/a	File[]
chrom_sizes	chrom_sizes	n/a	File
gencode.v46.annotation.gtf.gz	gencode.v46.annotation.gtf.gz	n/a	File

Steps

ID	Name	Description
3	pp.import_data	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
4	metrics.tsse	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
5	pl.tsse	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.5.3+galaxy2
6	pp.filter_cells	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
7	pp.add_tile_matrix	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
8	pp.select_features	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
9	pp.scrublet	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
10	pp.filter_doublets	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
11	Extract element identifiers	toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
12	Extract first dataset	__EXTRACT_DATASET__
13	Select first	Show beginning1
14	Filter collection	__FILTER_FROM_FILE__
15	Concatenate AnnDatas	toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0
16	pp.select_features on all	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
17	tl.spectral	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.5.3+galaxy2
18	tl.umap_no-batch-correction	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.5.3+galaxy2
19	pl.umap_no-batch-correction	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.5.3+galaxy2
20	pp.harmony	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
21	pp.mnn_correct	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
22	pp.scanorama	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.5.3+galaxy2
23	tl.umap_batch-correction	Recalculates UMAP-embeddings and adds it under the key 'X_umap_harmony' toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.5.3+galaxy2
24	tl.umap_mnn-correct	Recalculates UMAP-embeddings and adds it under the key 'X_umap_harmony' toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.5.3+galaxy2
25	tl.umap_scanorama	Recalculates UMAP-embeddings and adds it under the key 'X_umap_harmony' toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.5.3+galaxy2
26	UMAP-plot of X_spectral_harmony	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.5.3+galaxy2
27	pp.knn	Recalculates UMAP-embeddings and adds it under the key 'X_umap_harmony' toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.5.3+galaxy2
28	UMAP-plot of X_spectral_mnn-correct	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.5.3+galaxy2
29	UMAP plot of X_spectral_scanorama	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.5.3+galaxy2
30	tl.leiden	Recalculates UMAP-embeddings and adds it under the key 'X_umap_harmony' toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.5.3+galaxy2
31	UMAP-plot of Leiden Clusters	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.5.3+galaxy2

Outputs

ID	Name	Description	Type
tsse-plots	tsse-plots	n/a	File
collection_without_first_entry	collection_without_first_entry	n/a	File
out_png	out_png	n/a	File
x_spectral_harmony	x_spectral_harmony	n/a	File
x_spectral_mnn-correct	x_spectral_mnn-correct	n/a	File
x_spectral_scanorma	x_spectral_scanorma	n/a	File
anndata_harmony_leiden	anndata_harmony_leiden	n/a	File