filter/filter_with_scrublet

Description

Doublet detection using the Scrublet method (Wolock, Lopez and Klein, 2019). The method tests for potential doublets by using the expression profiles of cells to generate synthetic potential doubles which are tested against cells. The method returns a "doublet score" on which it calls for potential doublets.

For the source code please visit https://github.com/AllonKleinLab/scrublet.

For 10x we expect the doublet rates to be: Multiplet Rate (%) - # of Cells Loaded - # of Cells Recovered ~0.4% ~800 ~500 ~0.8% ~1,600 ~1,000 ~1.6% ~3,200 ~2,000 ~2.3% ~4,800 ~3,000 ~3.1% ~6,400 ~4,000 ~3.9% ~8,000 ~5,000 ~4.6% ~9,600 ~6,000 ~5.4% ~11,200 ~7,000 ~6.1% ~12,800 ~8,000 ~6.9% ~14,400 ~9,000 ~7.6% ~16,000 ~10,000

Type

python_script

License

MIT

Arguments

Name
Type & Properties
--input
file
required
--modality
string
--layer
string
--output
file
output
--output_compression
string
--obs_name_filter
string
--do_subset
boolean_true
--obs_name_doublet_score
string
--expected_doublet_rate
double
--stdev_doublet_rate
double