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Description
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 (1.2.0
and 2.0.0
):
/SC_ATAC_COUNTER_CS/SC_ATAC_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/
Cell Ranger ARC (1.0.1
and 2.0.0
):
RNA
/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/files/metrics_summary_json.json
ATAC
/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/
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