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Published 6 months ago • verified publisher icon aertslab

Add support for multiple Cell Ranger versions to calculate_saturation_10x_samples.py

Open cflerin opened this issue 4 years ago • 0 comments

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/

cflerin avatar Jul 19 '21 10:07 cflerin