Library Mito Fraction
Screen a bulk RNA library for elevated mitochondrial-read fraction.
Description
Mitochondrial-read fraction describes the share of mapped library reads assigned to mitochondrial sequences.
Mitochondrial-read fraction describes the share of mapped library reads assigned to mitochondrial sequences. A high fraction can have several biological or technical causes.1
Screen a bulk RNA library for elevated mitochondrial-read fraction.
When to use Library Mito Fraction
Use this tool to screen a bulk RNA library for elevated mitochondrial-read fraction.
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 Library Mito Fraction 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 mitochondrialMappedReads, allMappedReads, maximumMitoPercent using the field table and calculation rules, then run the tool.
- Read mitoPercent, nuclearAndOtherReads, contaminationFlag. 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 |
|---|---|---|---|
| mitochondrialMappedReads | Mitochondrial mapped reads | number | Required |
| allMappedReads | All mapped reads | number | Required |
| maximumMitoPercent | Maximum mito percent | number | Required |
Enter a positive mapped total and nonnegative mitochondrial count no larger than that total, plus a finite maximum criterion. Return mitochondrial percentage, the nonmitochondrial remainder and a strictly-above flag. Equality does not flag.
mito%=100 mitochondrialMapped/allMapped; flag=mito%>maximum Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| mitoPercent | Mito percent | number |
| nuclearAndOtherReads | Nuclear and other reads | number |
| contaminationFlag | Contamination flag | boolean |
{
"input": {
"mitochondrialMappedReads": 10,
"allMappedReads": 100,
"maximumMitoPercent": 15
},
"output": {
"mitoPercent": 10,
"nuclearAndOtherReads": 90,
"contaminationFlag": false
}
}Limitations and assumptions
The output name contaminationFlag is a threshold label rather than a causal diagnosis. No alignment, annotation or sample-quality recommendation is provided.
Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors. A successfully returned false flag is an evaluated outcome; its meaning is explained above.
Alternative or Complementary methods
Use Cell Mito Percent Filter: Gate each single cell by its mitochondrial UMI share. For a complementary task, use RRNA Contamination: Flag rRNA contamination in a sequenced RNA library.
References
-
Library Mito Fraction — tool.io
Similar or alternative tools
- Cell Mito Percent Filter
Gate each single cell by its mitochondrial UMI share.
- RRNA Contamination
Flag rRNA contamination in a sequenced RNA library.