Cell Mito Percent Filter

Gate each single cell by its mitochondrial UMI share.

Description

Mitochondrial UMI share is a per-cell quality summary.

Mitochondrial UMI share is a per-cell quality summary. Its interpretation depends on cell type and protocol as well as the supplied threshold.^[1]

Gate each single cell by its mitochondrial UMI share.

When to use Cell Mito Percent Filter

Use this tool to gate each single cell by its mitochondrial UMI share.

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 Cell Mito Percent 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 cellIds, mitochondrialCounts, totalCounts, maximumMitoPercent using the field table and calculation rules, then run the tool.
Read mitoPercents, retainedCellIds, failedCellIds. 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
cellIds	Cell ids	list of string	Required
mitochondrialCounts	Mitochondrial counts	list of number	Required
totalCounts	Total counts	list of number	Required
maximumMitoPercent	Maximum mito percent	number	Required

Enter aligned nonempty IDs, nonnegative mitochondrial counts and positive total counts, with mitochondria no larger than the corresponding total. Calculate percentages and partition IDs inclusively below/at the finite maximum versus strictly above. Preserve input order.

mitoPercent_i=100 mitochondrial_i/total_i; retain if percent≤maximum

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

Output field	Meaning	Value type
mitoPercents	Mito percents	list of number
retainedCellIds	Retained cell ids	list of string
failedCellIds	Failed cell ids	list of string

json

{
  "input": {
    "cellIds": [
      "a",
      "b",
      "c"
    ],
    "mitochondrialCounts": [
      10,
      30,
      5
    ],
    "totalCounts": [
      100,
      100,
      100
    ],
    "maximumMitoPercent": 20
  },
  "output": {
    "mitoPercents": [
      10,
      30,
      5
    ],
    "retainedCellIds": [
      "a",
      "c"
    ],
    "failedCellIds": [
      "b"
    ]
  }
}

Limitations and assumptions

No mitochondrial annotation, count normalization or universal QC cutoff is embedded. A failed threshold alone does not establish damage or contamination; duplicate IDs are not merged.

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 Cell Gene Count Filter: Filter single cells by detected gene-count threshold. For a complementary task, use Library Mito Fraction: Screen a bulk RNA library for elevated mitochondrial-read fraction.

References

Cell Mito Percent Filter — tool.io

Similar or alternative tools

Cell Gene Count Filter
Filter single cells by detected gene-count threshold.
Library Mito Fraction
Screen a bulk RNA library for elevated mitochondrial-read fraction.