Currently 10x multiome data (and some Cell Ranger versions) are not supported by calculate_saturation_10x_samples.py. There are different paths to the summary metrics file for multiome, RNA and ATAC, and these also differ between Cell Ranger versions.
Currently 10x multiome data (and some Cell Ranger versions) are not supported by
calculate_saturation_10x_samples.py. There are different paths to the summary metrics file for multiome, RNA and ATAC, and these also differ between Cell Ranger versions.Cell Ranger (incomplete list)
/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SUMMARIZE_REPORTS/fork0/files/metrics_summary_csv.csv(current implementation)Cell Ranger ATAC (
1.2.0and2.0.0):/SC_ATAC_COUNTER_CS/SC_ATAC_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/Cell Ranger ARC (
1.0.1and2.0.0):RNA
/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/files/metrics_summary_json.jsonATAC
/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/