Differential peak analysis with SnapATAC2
Version 1

Workflow Type: Galaxy

This workflow takes a cell-type-annotated AnnData object (processed with SnapATAC2) and performs peak calling with MACS3 on the cell types. Next, a cell-by-peak matrix is constructed and differential accessibility tests are performed for comparison of either two cell types or one cell type with a background of all other cells. Lastly, differentially accessible marker regions for each cell type are identified.

SEEK ID: https://workflowhub.eu/workflows/1089?version=1

Inputs

ID	Name	Description	Type
1	Cell-type #1	n/a	string
2	Cell-type #2	n/a	string
Cell-type Annotated AnnData	Cell-type Annotated AnnData	n/a	File
chrom_sizes_new.txt	chrom_sizes_new.txt	n/a	File

Steps

ID	Name	Description
4	macs3	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_peaks_and_motif/snapatac2_peaks_and_motif/2.6.4+galaxy1
5	cell-types_UMAP-plot	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1
6	merge_peaks	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_peaks_and_motif/snapatac2_peaks_and_motif/2.6.4+galaxy1
7	make_peak_matrix	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_peaks_and_motif/snapatac2_peaks_and_motif/2.6.4+galaxy1
8	Differential Expression between two cell types	Compares differentially accessible peaks between two cell types (f.ex. Memory B and Naive B cells) toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_peaks_and_motif/snapatac2_peaks_and_motif/2.6.4+galaxy1
9	Differential Expression compared to all cell types	Compares differentially accessible peaks between a cell type (f.ex. Naive B cell) and 30 random "background" cells of the other cell types toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_peaks_and_motif/snapatac2_peaks_and_motif/2.6.4+galaxy1
10	marker_regions	toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_peaks_and_motif/snapatac2_peaks_and_motif/2.6.4+galaxy1