Workflow: Cell Ranger Aggregate (RNA+ATAC)
Cell Ranger Aggregate (RNA+ATAC) Combines outputs from multiple runs of “Cell Ranger Count (RNA+ATAC)” pipeline. The results of this workflow are primarily used in “Single-Cell Multiome ATAC and RNA-Seq Filtering Analysis” pipeline.
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
ID | Type | Title | Doc |
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alias | String | Analysis name | |
threads | Cores/CPUs |
Parallelization parameter to define the number of cores/CPUs that can be utilized simultaneously. Default: 4 |
|
memory_limit | Integer (Optional) | ||
indices_folder | Directory | Cell Ranger Reference Sample |
Any \"Cell Ranger Reference Sample\" that builds a reference genome package of a selected species for quantifying gene expression and chromatin accessibility. This sample can be obtained from \"Cell Ranger Reference (RNA, ATAC, RNA+ATAC)\" pipeline. |
gem_well_labels | String[] | ||
normalization_mode | Library depth normalization |
When \"depth\" normalization is selected, subsample reads from higher-depth GEM wells until we equalize the 1) median number of unique fragments per cell for each ATAC library, 2) mean number of reads that are confidently mapped to the transcriptome per cell for each gene expression library. |
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annotation_gtf_file | File | ||
rna_molecule_info_h5 | File[] | Cell Ranger RNA+ATAC Sample |
Any \"Cell Ranger RNA+ATAC Sample\" that produces both gene expression and chromatin accessibility data from a single 10x Genomics library |
barcode_metrics_report | File[] | ||
atac_fragments_file_from_count | File[] |
Steps
ID | Runs | Label | Doc |
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aggregate_counts |
../tools/cellranger-arc-aggr.cwl
(CommandLineTool)
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Cell Ranger Aggregate (RNA+ATAC) |
Cell Ranger Aggregate (RNA+ATAC) |
cellbrowser_build |
../tools/cellbrowser-build-cellranger-arc.cwl
(CommandLineTool)
|
Cell Ranger ARC Count/Aggregate to UCSC Cell Browser |
Cell Ranger ARC Count/Aggregate to UCSC Cell Browser |
compress_raw_feature_bc_matrices_folder |
../tools/tar-compress.cwl
(CommandLineTool)
|
TAR compress |
TAR compress
========================================= |
compress_secondary_analysis_report_folder |
../tools/tar-compress.cwl
(CommandLineTool)
|
TAR compress |
TAR compress
========================================= |
compress_filtered_feature_bc_matrix_folder |
../tools/tar-compress.cwl
(CommandLineTool)
|
TAR compress |
TAR compress
========================================= |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
grouping_data | File | Example of datasets grouping |
Example of TSV file to define datasets grouping |
html_data_folder | Directory | UCSC Cell Browser data |
Directory with UCSC Cell Browser data |
cellbrowser_report | File | UCSC Cell Browser |
UCSC Cell Browser HTML index file |
web_summary_report | File | Cell Ranger Summary |
Report generated by Cell Ranger |
atac_fragments_file | File | ATAC fragments |
Count and barcode information for every ATAC fragment observed in the experiment in TSV format. |
atac_peaks_bed_file | File | ATAC peaks |
Locations of open-chromatin regions identified in this sample. These regions are referred to as \"peaks\". |
loupe_browser_track | File | Loupe Browser visualization |
Loupe Browser visualization file with all the analysis outputs |
aggregation_metadata | File | Aggregation metadata |
Aggregation metadata file in CSV format |
metrics_summary_report | File | Run summary metrics |
Cell Ranger generated run summary metrics in CSV format |
atac_peak_annotation_file | File | ATAC peaks annotations |
Annotations of peaks based on genomic proximity alone. Note, that these are not functional annotations and they do not make use of linkage with RNA data. |
raw_feature_bc_matrices_h5 | File | Raw feature barcode matrix, HDF5 |
Raw feature barcode matrix stored as a CSC sparse matrix in hdf5 format. The rows consist of all the gene and peak features concatenated together and the columns consist of all observed barcodes with non-zero signal for either ATAC or gene expression. |
aggregate_counts_stderr_log | File | Error log, cellranger-arc aggr step |
stderr log generated by cellranger-arc aggr |
aggregate_counts_stdout_log | File | Output log, cellranger-arc aggr step |
stdout log generated by cellranger-arc aggr |
filtered_feature_bc_matrix_h5 | File | Filtered feature barcode matrix, HDF5 |
Filtered feature barcode matrix stored as a CSC sparse matrix in hdf5 format. The rows consist of all the gene and peak features concatenated together (identical to raw feature barcode matrix) and the columns are restricted to those barcodes that are identified as cells. |
raw_feature_bc_matrices_folder | File | Raw feature barcode matrix, MEX |
Raw feature barcode matrix stored as a CSC sparse matrix in MEX format. The rows consist of all the gene and peak features concatenated together and the columns consist of all observed barcodes with non-zero signal for either ATAC or gene expression. |
secondary_analysis_report_folder | File | Secondary analysis |
Various secondary analyses that utilize the ATAC, RNA data, and their linkage: dimensionality reduction and clustering results for the ATAC and RNA data, differential expression, and differential accessibility for all clustering results above and linkage between ATAC and RNA data. |
filtered_feature_bc_matrix_folder | File | Filtered feature barcode matrix, MEX |
Filtered feature barcode matrix stored as a CSC sparse matrix in MEX format. The rows consist of all the gene and peak features concatenated together (identical to raw feature barcode matrix) and the columns are restricted to those barcodes that are identified as cells. |
https://w3id.org/cwl/view/git/69643d8c15f5357a320aa7e2f6adb2e71302fd20/workflows/cellranger-arc-aggr.cwl