UMI Collapse Rate

Calculate UMI duplicate collapse rate and reads per molecule.

Description

UMI collapse summarizes counts already assigned to unique molecules and repeated observations.

UMI collapse summarizes counts already assigned to unique molecules and repeated observations.^[1]

Calculate UMI duplicate collapse rate and reads per molecule.

When to use UMI Collapse Rate

Use this tool to calculate UMI duplicate collapse rate and reads per molecule.

Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.

How to use UMI Collapse Rate and understand its results

Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.
Enter rawBarcodeReads, uniqueMolecules using the field table and calculation rules, then run the tool.
Read duplicateReadsCollapsed, collapseRatePercent, readsPerMolecule. 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
rawBarcodeReads	Raw barcoded reads	integer; minimum: 0	Required
uniqueMolecules	Unique molecules after UMI collapse	integer; minimum: 0	Required

Enter positive integer raw and unique counts with unique≤raw; return collapsed count and both ratios.

duplicates=raw−unique; duplication%=100duplicates/raw; compression=raw/unique

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

Output field	Meaning	Value type
duplicateReadsCollapsed	Reads collapsed as duplicates	integer; minimum: 0
collapseRatePercent	UMI collapse rate (%)	number; minimum: 0; maximum: 100
readsPerMolecule	Raw reads per molecule	number; minimum: 0

json

{
  "input": {
    "rawBarcodeReads": 1000,
    "uniqueMolecules": 400
  },
  "output": {
    "duplicateReadsCollapsed": 600,
    "collapseRatePercent": 60,
    "readsPerMolecule": 2.5
  }
}

Limitations and assumptions

No sequence processing, UMI error correction or deduplication is performed.

Numeric inputs, where present, 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.

Alternative or Complementary methods

Use FRiP Score: Calculate fraction of mapped reads in peaks. For a complementary task, use Nucleosome-Free Fraction: Calculate the ATAC nucleosome-free fragment fraction.

References

UMI Collapse Rate — tool.io

Similar or alternative tools

FRiP Score
Calculate fraction of mapped reads in peaks.
Nucleosome-Free Fraction
Calculate the ATAC nucleosome-free fragment fraction.