COBRA Retention

Calculate COBRA restriction cut-site retention from band intensities.

Description

COBRA cut/uncut ratios summarize a restriction-retention assay signal.

COBRA cut/uncut ratios summarize a restriction-retention assay signal.^[1]

Calculate COBRA restriction cut-site retention from band intensities.

When to use COBRA Retention

Use this tool to calculate COBRA restriction cut-site retention from band intensities.

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 COBRA Retention 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 cutProductIntensity, uncutProductIntensity, minimumRetentionPercent using the field table and calculation rules, then run the tool.
Read totalIntensity, cutRetentionPercent, retained. 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
cutProductIntensity	Cut product intensity	number; minimum: 0	Required
uncutProductIntensity	Uncut product intensity	number; minimum: 0	Required
minimumRetentionPercent	Minimum cut-site retention (%)	number; minimum: 0; maximum: 100	Required

Enter nonnegative signals with positive sum and minimum percentage; return ratio and inclusive gate.

cut%=100cut/(cut+uncut)

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

Output field	Meaning	Value type
totalIntensity	Total product intensity	number; minimum: 0
cutRetentionPercent	Cut-site retention (%)	number; minimum: 0; maximum: 100
retained	Meets supplied retention threshold	boolean

json

{
  "input": {
    "cutProductIntensity": 75,
    "uncutProductIntensity": 25,
    "minimumRetentionPercent": 70
  },
  "output": {
    "totalIntensity": 100,
    "cutRetentionPercent": 75,
    "retained": true
  }
}

Limitations and assumptions

No digestion, conversion or methylation calibration is verified.

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. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use LUMA Methylation: Estimate LUMA methylation from normalized HpaII and MspI signals. For a complementary task, use Bisulfite Conversion Efficiency: Check bisulfite conversion efficiency from non-CpG cytosines.

References

COBRA Retention — tool.io

Similar or alternative tools

LUMA Methylation
Estimate LUMA methylation from normalized HpaII and MspI signals.
Bisulfite Conversion Efficiency
Check bisulfite conversion efficiency from non-CpG cytosines.