scripts/3.summarize-SBS.py
Summarizes SBS barcode calling and cell assignment across all sites: how many cells fall in each quality category, how many spots of each quality, and a total count of each called barcode (for comparison to NGS).
Does not respect overwrite_files.
Inputs¶
| Input | Description |
|---|---|
summary_data/{data_set_name}_sitelist.json | From step 2 |
SBS/{plate}-{well}-{site}/processed_SBS.tsv.gz | From step 1 |
SBS/{plate}-{well}-{site}/site_stats.json | From step 1 |
SBS/{plate}-{well}-{site}/{plate}-{well}-{site}_cell_quality_summary.csv | From step 2 |
Config used: data_sets, cell_quality_method, keep_cell_qualities (experiment); summarize_SBS.allowed_skips, process_SBS.barcode_col, core.cell_quality_column (defaults). See Configuration.
Outputs¶
| Output | Description |
|---|---|
summary_data/Total_Barcode_Calls_Counts_{data_set_name}.tsv | Count of cells/calls per barcode for each data set |
summary_data/Total_Barcode_Calls_Counts_WholeExperiment.tsv | Same across all data sets |
summary_data/Data_Stats_{data_set_name}.json | Totals of spots, cells, and quality categories per data set |
summary_data/Data_Stats_WholeExperiment.json | Same across all data sets |
summary_figures/plate_layout_PassToFailRatio_{data_set_name}.png | Ratio of cells passing to failing quality, per site laid out as the plate |
summary_figures/plate_layout_PassToFailRatio_0empty_{data_set_name}.png | Same, excluding Empty cells from failures |
summary_figures/plate_layout_PercentEmpty_{data_set_name}.png | Percent of cells without SBS information |
summary_figures/Quality_Cells_by_data_split, _by_well, _all_data | Cell quality category summaries at each grouping |
summary_figures/Quality_Spots_by_data_split, _by_well, _all_data | Spot quality category summaries at each grouping |