Differential peak analysis with SnapATAC2 Version 1
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Run on GalaxyThis 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.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| 1 | Cell-type #1 | n/a |
|
| 2 | Cell-type #2 | n/a |
|
| Cell-type Annotated AnnData | Cell-type Annotated AnnData | n/a |
|
| chrom_sizes_new.txt | chrom_sizes_new.txt | n/a |
|
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 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| marker_regions | marker_regions | n/a |
|
| marker_regions-plot | marker_regions-plot | n/a |
|
Version History
Version 1 (earliest) Created 2nd Aug 2024 at 19:23 by Timon Schlegel
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Created: 2nd Aug 2024 at 19:23
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