Empty Droplet Filter

Classify droplets by a caller-supplied minimum UMI count.

Description

A minimum-UMI screen partitions droplets by observed count.

A minimum-UMI screen partitions droplets by observed count. This simple threshold is distinct from testing whether their profiles differ from ambient RNA.^[1]

Classify droplets by a caller-supplied minimum UMI count.

When to use Empty Droplet Filter

Use this tool to classify droplets by a caller-supplied minimum UMI count.

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.

How to use Empty Droplet Filter and understand its results

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
Enter dropletUmis, minimumCellUmis using the field table and calculation rules, then run the tool.
Read cellIndexes, emptyIndexes, cellFraction. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
dropletUmis	Droplet umis	list of number	Required
minimumCellUmis	Minimum cell umis	number	Required

Enter a nonempty nonnegative UMI-total list and nonnegative minimum. Return zero-based indices in both partitions and retained percentage. The field cellFraction is expressed as 0–100 percent, not 0–1; threshold zero retains every droplet.

cell if UMI≥minimum; empty if UMI<minimum; cellFraction=100 cellCount/dropletCount

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
cellIndexes	Cell indexes	list of number
emptyIndexes	Empty indexes	list of number
cellFraction	Cell fraction	number

json

{
  "input": {
    "dropletUmis": [
      10,
      100,
      500
    ],
    "minimumCellUmis": 100
  },
  "output": {
    "cellIndexes": [
      1,
      2
    ],
    "emptyIndexes": [
      0
    ],
    "cellFraction": 66.66666666666666
  }
}

Limitations and assumptions

No ambient-profile likelihood or statistical EmptyDrops method is implemented. A threshold label does not establish viable cells or exclude doublets.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Ambient RNA Correction: Subtract a caller-estimated ambient RNA component from cell counts. For a complementary task, use Doublet Suspicion Score: Compare a cell’s expression profile with simulated doublet and singlet neighbors.

References

Empty Droplet Filter — tool.io

Similar or alternative tools

Ambient RNA Correction
Subtract a caller-estimated ambient RNA component from cell counts.
Doublet Suspicion Score
Compare a cell’s expression profile with simulated doublet and singlet neighbors.